Wednesday, June 16, 2010

DNA contamination and DNA cold hits

Part XVII in the Knox/Sollecito case

This post returns to the problem of forensic DNA contamination. It also addresses the problem of partial profiles and adventitious matches, especially with respect to cold cases. North Carolinians might want to take special note of the John Puckett and Raymond Easton cases, inasmuch as North Carolina may join other states in demanding DNA samples upon arrest. My prediction is that as the size of a DNA database grows, we will see a greater number of cold case convictions that turn out to be erroneous.

Murder of Jane Mixer
We have previously encountered the conviction of Gary Leiterman of the murder of Jane Mixer. The presence of both Mr. Leiterman’s DNA and that of John Ruelas. The prosecution was unable to come up with a reasonable explanation for Mr. Ruelas’ DNA; he was four years old at the time and lived in another city.

Dr. Theodore Kessis reexamined the DNA forensics of this case:
“Review of the electropherograms associated with this negative control sample (NEG 041902) reveals that it was contaminated, a fact that cannot be disputed since Dr. Milligan himself labeled it with a note indicating as much (Appendix 8 - Electropherogram sample NEG 041902).
Remarkably, Dr. Milligan stated in his 7/15/02 testimony that no contamination events had occurred during the course of his testing and that if any had, he would have documented them in his reports (pg. 141-21 and 142-4). Equally difficult to rectify here is the fact that when asked if he had ever committed an error, Dr. Milligan's replied he could never recall making one. (pg. 162, lines 1-5)”

While agreeing with others that most contamination events happen when two samples are handled closely in space and time, Dr. Kessis also offered a caution, “It must be noted however that contamination errors have been documented where no direct processing link between sample and contaminant have been established, raising the specter that a source of contamination can linger in a laboratory for some time.”

Dr. Kessis found another deficiency: “As previously mentioned, Corrective Action files and Error logs form an important part of a laboratory's quality control and assurance programs by centralizing the documentation of errors within the laboratory. Mandated by the DAB Standards (Appendix 2, section 14.1.1), such data allows laboratory management to quickly and efficiently identify and address systematic problems that affect the reliability of testing results.”

“Given the thousands of samples, hundreds of cases, and number of people handling casework within this laboratory, the lack of a centralize system to track errors and discrepancy indicates that the lab had no mechanism in place to identify and deal with systematic problems such as contamination events.”

There are several take-home messages for students of the Knox/Sollecito case here. Contamination by more than one individual’s DNA is possible. The laboratories in question will sometimes claim to be error-free, as did the Rome lab. In such an instance it would be helpful to check the laboratory’s corrective action files, which are more likely to be accurate than someone’s memory. Whether the Rome lab has such files is unclear. Finally, when DNA results force one to an absurd conclusion (as with the kitchen knife), contamination or misinterpretation should be suspected.

The case of Gregory Turner
Gregory Turner was indicted and jailed for a murder when the DNA from a murdered woman in Newfoundland was found on his wedding ring. The ring also contained DNA from one other contributor, thought to be his accomplice. However, the lawyer sought out the names of the technicians from the lab and determined that the technician working on his ring also worked on the victim’s fingernails. Moreover, the DNA from the second contributor to the ring turned out to be the profile of the technician herself. After many months, Mr. Turner was released from jail. This particular case of DNA contamination is an example of where both primary and secondary transfer of DNA occurred. As did the Mixer case, it shows that contamination can transfer the DNA from more than one person onto an item of evidence. This is worth bearing in mind given the multiple DNA contributors to the bra clasp in the Knox/Sollecito case.

Profile N
As was true in the Jaidyn Leskie case, the victim of one crime can become a suspect in other crimes on the basis of contaminated DNA evidence. Sometimes it takes a major foul-up to prod a laboratory into corrective action. In New Zealand, the Wellington police were investigating two murders, dubbed Rex and Pad, as well as N, the victim of an assault.

Michael Strutt reported, “One caught up in the testing was a mild mannered Christchurch man who had been assaulted outside his local, the Hagley Arms Hotel, on 23 April 1998. Police had taken blood in order to eliminate his DNA from samples taken from the scene of the assault and sent it to ESR for testing. The result of this test came to be dubbed 'Profile N' by the inquiries which were to follow… The Christchurch assault victim was subjected to 'extensive police inquiries' for more than three months and his financial records were seized. This established what he had claimed all along, that he had not left Christchurch around the time of the murders. In fact he hardly left Christchurch at all… Although they never discovered exactly how the mistakes had happened they did determine that the 'Rex' and 'Pad' samples had been accidentally contaminated with DNA from Profile N at an early stage of processing at ESR's Mt Albert laboratories. Extracts from them sent to other laboratories for testing also returned Profile N. Numerous recommendations for improving oversight, record keeping and even laboratory ventilation were made.”

“During the inquiry ESR [Environmental Science & Research Ltd] was asked to check the results of all testing done in July 1998 for any further instances of Profile N. Although they initially reported that none were found, later retests showed a partial profile consistent with N in another sample from 'Pad'. They also revealed 25 other 'unexplained' profiles in 14 of the 36 samples tested that month.”

A group investigating these cases asked a manager of the forensic unit of the ESR lab to comment, “The Wellington murders you refer to were not DNA failures. The problem was picked up and investigated. Five separate investigations failed to find scientific proof for the cause of the anomalies. No direct evidence of either accidental or deliberate contamination has come to light. Existing facilities and protocols were shown to meet independent quality audit requirements. The Ministerial Inquiry recognising the points above concluded that on the balance of probabilities the apparently anomalous results could be ascribed to accidental contamination of DNA extracts within the ESR laboratory. They made a number of recommendations which ESR has either implemented or is planning to implement. This sits comfortably with our continuous improvement management focus.”

The fact that the lab in question met the audit requirements is evidence that simply following accepted protocols does not guarantee that contamination will never happen. The lack of the determination of an exact mechanism of contamination is consistent with Dr. Kessis’s caution in the Mixer case above. People who argue that Amanda Knox and Raffaele Sollecito are guilty sometimes demand a mechanism of contamination; unfortunately, this cannot always be determined.

The first false cold hit case in the UK
Michael Strutt wrote, “A man [Raymond Easton] with advanced Parkinsons disease who could not drive an automobile or dress himself unaided was linked to a burglary which had occurred 200 miles from his home. In spite of protestations of innocence and alibi evidence police arrested him because the DNA profiles matched and 'so it had to be him'. It was several months before10-point DNA tests were done on samples from the suspect and the crime scene. The results exonerated him.

He gained his freedom and a brief note from the prosecutor saying that charges were being dropped because ‘there was not enough evidence to provide a realistic chance of conviction’. He still awaits an official apology. Or even an admission of error.”

The reason why Mr. Easton was initially suspected was an adventitious match, as opposed to contamination. This case shows that adventitious matches can happen especially for partial profiles. The first profile had only six loci, but the second profile had 10 loci. As with DNA contamination, when a cold hit match leads to an absurd result, the DNA evidence needs to be reconsidered.

The Sylvester murder, a cold hit combined with a partial profile
According to Dr. Donald Riley, “A partial profile is one in which not all of the loci targeted show up in the sample. For example, if 13 loci were targeted, and only 9 could be reported, that would be termed, a partial profile…Over-interpretation of partial profiles can probably lead to serious mistakes. Such mistakes could include false inclusions and false exclusions, alike.” Let us examine the rape and murder of a young nurse which ultimately yielded a partial profile of the assailant many years later.

Diana Sylvester was raped and murdered in San Francisco in 1972. After evidence in this case was subjected to forensic DNA analysis, a trawl through California’s DNA database identified a suspect over thirty years later, a cold hit. Of the investigations treated here, the Sylvester murder is the one in which the particulars of the investigation (a cold hit) and the differences in expert opinion on the correct statistical calculation have the least relevance to the Knox/Sollecito case. However, several more subtle points in common can be found.

In this case the suspect was identified on the basis of his DNA matching a partial profile from evidence taken from the victim. This suspect, John Puckett was in the DNA database because of his convictions for rape about five years after Ms. Sylvester was raped and murdered. However, the MO of the crime was consistent with another rapist, Robert Baker, who matched the physical description of the assailant better than Mr. Puckett and who was deceased by the time the case was reopened. The defense was barred from introducing information about Mr. Baker, the original suspect. Over the objections of the defense, the prosecution was allowed to bring in Mr. Puckett’s past convictions. How strong was the DNA evidence against Mr. Puckett?

The main issue in this case is a disagreement among experts over the correct statistical calculation to use in cold hit cases. Another key element in this case is that it made use of a partial, not full, DNA profile. In the United States a full DNA profile has thirteen separate markers (loci). A profile must have seven markers for it to be searched in California’s database. However, only 5 and a half markers were clearly found in the Sylvester murder. The jury was told that the chances of a random person’s matching the DNA found at the crime scene were 1.1 million to one. Yet when the odds were calculated with a different set of statistical assumptions the odds were only one in three, a statistic that the jury was barred from hearing. This is why the odds were only 1.1 million to one, and not substantially higher. However, when one uses a model that takes into account that there were 338,000 profiles in the database, one arrives at the 1-in-3 odds. The question of which model is better is a difficult one, yet it is odd that California courts have taken it upon themselves to decide which model is more appropriate. And the difference between one in 1.1 million and 1 in 3 is huge. It would have probably been enough to move at least one juror from guilty to not guilty beyond a reasonable doubt.

A second issue concerns the number of loci in profile itself. The peaks that were needed to flesh out the profile from 5.5 loci to 8 loci fell below the laboratory’s intensity threshold, but forensic technician Bonnie Cheng wished to interpret them anyway. DNA profiles contain artifact peaks, some of which are known as blobs and others as stutters. Deciding which peaks are true and which are artifacts may contain an element of subjectivity. The prosecution’s outside DNA witness, Dr. Chakraborty used Mr. Puckett’s full profile to interpret the partial profile, a practice that is open to serious question.

A third issue is that the sample was mixed, containing DNA markers from both the victim and assailant. The question of which markers belong to which profiles naturally arises. DNA forensic expert Peter Gill said, “If you show 10 colleagues a mixture, you will probably end up with 10 different answers.” With reference to this case Dan Krane made an important point, “There is a public perception that DNA profiles are black and white. The reality is that easily in half of all cases—namely, those where the samples are mixed or degraded—there is the potential for subjectivity.”

A fourth issue is that the lab used up so much of the sample that the defense could not do its own testing. This is a debatable practice in a DNA case; some guidelines indicate that this should not be done unless the defense agrees in advance.

One lesson for students of the Knox/Sollecito case is that the judge’s decisions might control the outcome of a case. The judge’s decision to exclude one statistical model in the Puckett case can be compared with Judge Massei’s decision not to order an independent review of the forensics of the Knox/Sollecito case. A second message is that DNA profiling is not immune to cognitive bias. In both the Puckett case and the Knox/Sollecito case, the forensic technicians lowered the bar with respect to the intensity threshold. A third fact to bear in mind is that Meredith’s DNA profile from the kitchen knife was a partial profile. However, how many loci should be counted for this piece of evidence depends entirely upon one’s choice of intensity threshold. Fourth, the bra clasp is a mixed sample, and interpreting mixtures contains an element of subjectivity.

Some possible reforms

Australian criminal defense barrister Peter Faris wrote in response to the Benjamin Forbes case, “Faced with a figure of 10 billion, a jury will always convict. The only way that it can be defended is for the defence to demonstrate a doubt arising from contamination, forensic or statistical procedures. In the real world, defence lawyers and legal aid bodies are just not equipped to investigate these matters. Many cases rely (to a greater or lesser extent) on DNA evidence. In some of them, such as Forbes, there is simply no other evidence. Consequently, if there is contamination at the scene, in police or laboratory storage or in the laboratory itself, the defence can never prove it.

Mr. Faris proposed some reforms:
“DNA should never be admitted unless there is corroboration: that is, there must be some other evidence of the identity of the offender. As for the rest of DNA cases, the solution is to put the burden on the prosecution. This can be done by amending the various Evidence Acts around the country to make DNA evidence inadmissible unless the trial judge is first satisfied, by the prosecution, that it should be admitted. The prosecution should apply to the trial judge, in a preliminary hearing, to admit DNA evidence. They must satisfy the judge, on the balance of probabilities, of various matters. The important matters are that the burden of admissibility is upon the crown. No DNA evidence could be led unless this procedure has been completed.
Conditions could be imposed in the legislation to protect the accused. For example, the prosecution would be required to produce evidence to disprove contamination, whether at the scene or in the laboratory. Strict proof of continuity of exhibits would be required. The prosecution would have to call evidence of the current international statistical procedures. Proof by the defence of international articles and learned writings could be relaxed.”

Final Thoughts
We have examined the problems with clerical errors, contamination, statistical manipulation, and outright fraud in this and preceding posts. It must also be borne in mind that the presence of DNA on an object rarely provides information on the time or means (primary, secondary, etc.) of its deposition. Paradoxically, DNA profiling is the branch of forensics with the firmest grounding in science. Much evidence exists to the effect that it is held in particularly high esteem by juries (a possible subject for a future post).

Taking all of these issues into account, I would not convict someone in a case where the sole piece of evidence comes from DNA forensics, but I would give it considerable weight, provided that the data were obtained legitimately and presented to the court in a transparent manner that respected the discovery rights of the defense. The worthy question of whether or not states should demand DNA samples upon felony arrest is outside the scope of this post.


RoseMontague said...

A terrific post, Chris. I know you were not approaching the subject of mandatory DNA samples and privacy issues, but your entire post argues against it.

Anybody that gives a voluntary DNA sample after reading this post is asking for trouble, in my opinion. Going back to the Duke Lacrosse case, in retrospect, the players that lined up to give samples were fortunate indeed that their DNA did not end up mixed with Crystal's in one test or another.

Of course, their DNA is now in a database (my assumption-perhaps you can answer) so there is no guarantee that this might not come back to haunt them.

Chris Halkides said...


I agree with your point about contamination. I do not know whether the entire team's samples were included into the database or not. And the law may be different with respect to a nontestimonial order versus a conviction. However, if North Carolina demanded samples upon arrest in 2006, then samples from the three accused players would now be in the database.

I included the discussion of cold hits and partial profiles partly because I am conversing with someone whose relative was convicted on the basis of this kind of evidence.


Anonymous said...


This was a very interesting post on DNA.

Do you have a link (perhaps to an earlier post - I think I read it here but am not sure) containing Meredith's DNA profile on the knife? Was her partial profile obtained before LCN testing or after?


At JREF I thought I read that if a voluntary DNA sample is given it must be destroyed after a time and not applied to a database. Is that not true?

I have wondered when Knox and Sollecito were asked to give a DNA sample (before or after incarceration) and if anyone else was asked to give samples voluntarily.


Anonymous said...

I included the discussion of cold hits and partial profiles partly because I am conversing with someone whose relative was convicted on the basis of this kind of evidence.

Presently, are convictions occurring based on partial profiles? Hopefully, if this conviction was some time ago it can be reviewed against new standards.

Is there a scientific community standard that agrees what constitutes a profile that should be considered as evidence in a case, (in evidence collected and tested - either too low a number of loci to compare against a defendant's profile so it shouldn't be considered; or a high number of loci match a defendant's profile so it should be considered).


RoseMontague said...

The FBI maintains a central DNA database called CODIS, if I am reading this correctly. The type of profiles that make it into the system appear to vary by state.

Link to follow:


Chris Halkides said...

Christiana at 12:07,

I do not think that there is any particular number of loci that is an agreed upon minimum to convict, since a match probability can be calculated regardless. However, California law is that one needs 7 loci to search the database, so that might be a de facto minimum in a cold case.

Indeed partial profiles are enough to convict here and in other countries. One defense attorney in a link I gave said words to the effect that the jury has only to hear the word "match," and they will convict. The case I mentioned is being appealed.


Chris Halkides said...

Christiana at 11:44 AM,

Meredith's partial profile was the result after the LCN amplification. There is an electropherogram on page 5 of the Johmson/Hampikian open letter. Perugia Murder FIle also has some images of the profiles here

How many of the peaks on the knife should have been counted is a tricky question that I tried to tackle in a previous post and one before that.


Chris Halkides said...


What is really scary to contemplate is Gottlieb getting his hands on DNA evidence.


Chris Halkides said...

Joseph Bishop commented on an article in the National Review. The NR took a what-is-wrong-with-the-youth-of-today stance with respect to the Knox/Sollecito case. Mr. Bishop’s response ended with a criticism of the University of Washington for not taking a stronger stand in defense of Ms. Knox. Duke lacrosse veterans in particular may want to comment on this.

Debrah said...

"Duke lacrosse veterans in particular may want to comment on this."

Wow, Chris.

That's certainly a provocative topic.

At the risk of stepping on your toes a bit (Ha!), I think it can be said that the academy, in general, is not comprised of those whose first instinct is to wander outside the box and risk their own comfort level.

It would seem that a university is run rather like a business.....while putting on a facade of altruism and enlightenment.

Positions taken are those of least resistance and once positions are taken regarding society's "culture wars" there's little deviation by members of the academic "club".

But such an insular club it is.

I've always been perplexed by the fact that those who profess to teach seem to have so little experience about life, in general.

This perhaps creates the unusually powerful strain of insularity that we often witness from members of the academy.

They exist inside a fragile shell that can be cracked so effortlessly if they dare go against accepted views.

The very strong quadrumvirate of ( race / class / gender / sexual orientation ) reigns.

In the Duke Lacrosse Hoax, we saw race/class/gender rule.

In the Frank Lombard case---the high Duke official convicted of horrific molestation of the boys he adopted---we witnessed how sexual orientation is one of the very powerful "untouchables" within the academy as well as in the media.

Can anyone imagine how all of those same people would have reacted if the straight lacrosse players had done anything close to what Lombard did?---a member of Duke's staff, no less!

And it must be highlighted that there seems to be a sexist twist to the way lesbians are covered as compared to the way gay men are covered in the media and beyond.

Rabid feminists and lesbians inside the academy who went after the lacrosse players were lambasted nonstop (and for good reason!) and with glee; however, gay men didn't receive quite the same brand of ridicule.

Even though a few gay male bloggers and writers were some of the most egregiously offensive when the case broke.

The writer Allan Gurganus and gossipy blogger Andy Towle were chief among them.

Yet, did we see a grand call for these hetero-male-hating bigots to apologize?

Did they apologize at all?

Chris, regarding the University of Washington not taking a stronger stance, one should not be surprised.

Unless Knox and her family had direct ties to the university or were tethered to an aspect of the academy's "untouchable" quadrumvirate of ( race / class / gender / sexual orientation ) in a way that would formulate a high profile of "victimhood"......

.......and her alma mater could come off in the media as her "champion" or "hero"......

.......then getting involved would have been of no benefit to them.

Moreover, the university would hardly go on record for attacking a European city and its justice system.

Why....that's just not done!

Chris Halkides said...


One option for UW would be to affirm the right to due process, which surely includes the right to see and to challenge the evidence against oneself. Readers of this blog know that I feel the Italian law enforcment (ILE) and judicial authorities came up way short, especially with respect to the log files and electronic data files with DNA information.

We also know that much of what Amanda Knox said in her diary was leaked in bad translations. Other leaks consisted of patently false information. If UW itself did not want to criticize ILE for these actions, how about individual faculty members?

Finally, Amanda Knox is a woman, and one whose normal sexual activity has been turned into something evil. Let's not forget the headline upon her conviction:

The Kercher Trial: Amanda Knox snared by her lust and her lies.


Debrah said...

I agree, Chris.

Knox was certainly treated unfairly in the media right from the start.

However, in her case, it was as much sensationalism as sexism.

If she were a guy caught up inside a murder case where sex was reported as being a prominent feature, I think the media and the bloggers would have used that element in the same way.

And it would have been so much easier to discern all motives in this case had the language barrier not existed for many.

I agree that individual professors at the U of W---those who have tenure (LOL!)---should have spoken out in her defense. Especially those who knew her well.

You might not agree; however, Knox's own behavior did not help her case.

That cannot be blamed on the media or on detractors.

Chris Halkides said...


More than some of her supporters perhaps, I agree that some of Ms. Knox's actions were odd or inappropriate. However, I would raise two points in her defense. She was clearly frightened and exhausted by 5 November 2007, probably earlier. Therefore, I would say that there were some extenuating circumstances. I also believe that some of the actions that Dr. Giobbi found suspicious were entirely inoccuous, such as her alleged swiveling of her hips when she put on her shoe covers.


Debrah said...


Yes, Chris.

Some of the things that were chosen to sensationalize the case were comical and insignificant; however, that's the unfortunate game played by the media---both tabloid as well as the so-called "mainstream" variety.

I won't revisit the conversations we've had here in the past......just to say that, in my opinion, the reality or the "truth" lies somewhere in between.

Anonymous said...

Joseph Bishop commented on an article in the National Review. The NR took a what-is-wrong-with-the-youth-of-today stance with respect to the Knox/Sollecito case. Mr. Bishop’s response ended with a criticism of the University of Washington for not taking a stronger stand in defense of Ms. Knox. Duke lacrosse veterans in particular may want to comment on this.


Was Amanda still affiliated with UW at the time of her studying in Perugia? Was she enrolled in a joint program between the two universities? I wasn't sure if her time in Perugia was a continuation of her studies at UW or she had taken a sabbatical at UW to study abroad on her own.