Problems with DNA profiles - 3

Problems with DNA profiles - 3

If you found this file in an archive then use keyword "nutteingy3" in a search engine to find an updated version or related pages.
Articles posted to moderated Yahoo community group for forensic science personel under my nom de guerre of Nona Revers or as it turns up there nonarevers.
Text in brown is my contribution - due to the nature of such dialogues the thread can get rather broken as it splits into different sub-themes at different times and involving different people. Yahoo forensic science group
A more searchable archive of that group
The following like the first "y" file can get a bit jumbled, and probably sections missing, for anyone wanting the original question/reply structure then please consult the archives on http://infoarchive.net/sgroup/forensic-science/

Freezing DNA nonarevers

There is nothing in IJLM back to 1997 (earliest on line) and nothing in FSI back to 1983 concerning validity of recovery of old DNA stored at ambient temp and humidity, let alone comparing with current donated samples from the same original sources. Unless it is tucked away in a corner of an article with not the slightest reference in the title.

What I was thinking is that there have got to be suspect and elimination profiles from 1985, when DNA testing came into forensic use, even if its just 100 with surviving donors. Wouldn't a good validation study be to run PCR, RFLP, and STR profiles on 2005 samples from these people and see if they are the same. Maybe that's already been done somewhere?

That sounds quite logical. While the DNA is not tested for forensics, it is tested to meet strict guidelines of parentage. So if the parentage is questioned is this the general procedure they follow - run DNA on the frozen semen, run DNA on the offspring, and run DNA on the mother?

Of course, semen is a more complex mixture that is buffered by the other constituents of semen than plain DNA - but it does show that a semen stain from 30 years ago stored in a freezer would give the same results as fresh semen.

Bellow is a link to a recent presentation by my colleague, Margaret Kline, about her experiences with long-term storage of DNA. Several references can be found within the presentation. Margaret has been testing several stains at various conditions (including liquid nitrogen -150 oC... now that's freezing!). Stains stored at room temp will begin to show some degradation over time (no shock there), but typeable DNA was recovered from stains at all samples examined.

As far as potential errors in junk DNA regions due to freeze/thawing, here is my speculation...

Let's suppose that a tube containing 1ng of DNA undergoes several rounds of freeze/thawing. Suppose that the genotype at TH01 in the fresh sample of this individual is 8, 9.3. In 1 ng of DNA, there are approximately 167 total pairs of chromosomes (one cell = 6pg of DNA; 1 ng = 1000pg / 6pg = 166.7 cells). Thus, to believe that freezing and thawing can affect the genotype, on the 167 chromosomes that have an 8 allele at TH01, nearly each and every locus would have to spontaneously have to "mutate" (due to less overall robustness - not sure what that means) to say a 7 allele. Meanwhile... the other 167 chromosomes will "mutate" from a 9.3 allele to... I don't know 9... 10... 11... you get the point. In a sea of 3 billion nucleotide bases only a thimbleful of bases changes occur in the junk regions (I'm not sure of the mechanism here since the cellular enzymes have been inactivated or removed during extraction) of forensically chosen markers to "mess up" genetic profiles.

I think it's easier to believe that DNA can degrade from repeated freeze/thawing by shearing rather than the spontaneous generation of novel alleles.

Here is the link I mentioned earlier... http://www.cstl.nist.gov/biotech/strbase/pub_pres/KlineMarch2005storageDNA.pdf

All the following is just speculation for consideration. The DNA sections chosen for profiling are in the so-called "junk DNA" areas, where not only are there DNA repeats, but on human evolution time-scale there has been enough mutations to be of use for identity purposes. To me this would suggest that such DNA is not as robust as the "active" DNA. Errors in this DNA , due to stress conditions for example, would not be significant for biological inheritance. But errors in the junk DNA, due to freezing and un-freezing, will not necessarily lead to unviable dogs or humans but could mess up adduced profiles.

Another consideration, harking back to a fundamental assumption. To multiply allele frequencies together, an implicit assumption is made, that all loci/allele inheritance are independent of all others. The "junk DNA" may be involved with (computer parlance) error correction/parity checks cross- coupled to "active" DNA. http://www.nature.com/news/2002/020916/full/020916-4.html by Donall Mac Donaill , subsciption now, or discussed on http://www.idthink.net/biot/error/

There is not even validation study into biological material that has been frozen for 20 years and then tested against current samples from the same contributors. Let alone study of stored material at ambient conditions.

In FSI 112 (2000) page 157 one study into one 17 yearold blood stain stored at ambient which showed the 'heavy' loci D18 and D2 responses so depleted over 17 years as to be almost forensically unuseable. Responses of about 3000 rfu for D19 gradually reducing in peak heights down to D18 and D2 peaks of about 150 rfu . Even that single reported analysis did not have a comparison with a current sample from the same person to check for any changes.

By pure coincidence I saw this report today concerning loss of frozen state for just 4 days. Quote http://www.abqtrib.com/albq/nw_local/article/0,2564,ALBQ_19858_3705941 ,00.html

Freezer error prompts query from victims More than 60 cases are connected to the temporary meltdown in the Police Department's evidence room. By Joline Gutierrez Krueger Tribune Reporter April 16, 2005 Officials with the District Attorney's Office are attempting to allay crime victims' fears that their cases could be in jeopardy because of a freezer malfunction in the Albuquerque Police Department evidence room.

But whether the victims' cases are among the more than 60 cases District Attorney Kari Brandenburg says are involved in the temporary meltdown two months ago, advocates say the fallout could be emotionally wrenching for victims.

"It's tragic because it not only affects those victims whose cases might directly be connected to the evidence that is destroyed but every victim that has a pending case out there," said Elena Giacci, executive director of the Coalition to Stop Violence Against Native Women. "They start worrying: `Could it be my case? Could my attacker go free?' It brings up the whole trauma again, the emotion that's attached."

Brandenburg says her office has begun to review a list of 1,644 items police said were in the evidence room's faulty freezer to determine what cases were affected.

A list of between 60 and 64 cases was completed Thursday, she said. Of those, most are still pending or have recently been tried or pleaded out, she said.

At least 15 are murder cases, and nine are rape cases, she said. Sandy Dietz, director of the District Attorney's Office Victim Impact Program, said she and her victim advocates are contacting every victim or family member whose case is on the list. "People are worried until we begin to explain to them exactly what happened and exactly what is being done," Dietz said. Prosecutors involved in each case are also speaking with victims and families, she said. The freezer went down during the weekend of Feb. 19. The problem was discovered Feb. 22, and the freezer repaired Feb. 23, Brandenburg said she learned from a police memo. A freon leak caused the shutdown, said police Capt. Larry Sonntag, supervisor of the Metropolitan Forensic Science Center. <...> End Quote

Yes, it was routine for long term storage of biological samples to be in a freezer in 1984. That was the year I began training as a crime scene investigator, and the two long term storage options that I recall were drying out the sample or freezing it. I don't know that aren't validation studies of DNA stored for 20 years, they would be simple enough if the contributors of some of the stored DNA were still alive.

Ho-hum here we go again

Why do I still keep seeing such reports? http://www.macleans.ca/topstories/news/shownews.jsp?content=n061443A June 14, 2005 - 17:11

Defence expert slams RCMP handling of DNA in 30-year-old murder case

AMY CARMICHAEL VANCOUVER (CP) - A blood sample used to link murder suspect Robert Bonisteel to the stabbing deaths of two 14-year-old Vancouver girls in 1975 was mishandled by the RCMP, a DNA expert said Tuesday.

The speck of blood found on Bonisteel's shoe, smaller than a dust particle, was kept in unsealed bags that could easily be contaminated, said Dr. Ron Riley. "It's so easy to contaminate a sample with such a small amount of DNA," said Riley, who was testifying for the defence in B.C. Supreme Court. "It happens in many labs, it's written about all the time. It's a limit of the technology. The sample in this case is just so small I don't think it's scientifically significant. To use it as the foundation of a probable match, I think that's a mistake."

Bonisteel is charged with first-degree murder in the stabbing deaths of Judy Maria Dick and her friend Elizabeth Inge Zeschner. It took 26 years of testing the sample and considerable advances in DNA science to finally obtain a partial profile suggesting the blood on Bonisteel's shoe belonged to one of the teen victims. The sample, just six or seven human cells, degraded over time and was too small to be reliable, said Riley.

"They're going below the threshold used by other labs and that's risky. It's such a small amount I don't think it's reliable." According to lab reports, RCMP scientists placed the fragile matter in uncapped tubes in a spinning centrifuge, right beside samples from the victims. This is done to concentrate the samples, but they should be sealed during the process, Riley said.

Court has also heard the samples were handled by staff who didn't change gloves between touching the victims' bra and sweater and then picking up Bonisteel's shoe. The Crown accused Riley of having idiosyncratic views not shared by anyone else in the scientific community. Experts for the prosecution have told court the odds of the analysis being wrong are one in 14 billion.

Even with all the alleged mistakes, Riley said the likelihood that the blood on Bonisteel's shoe could belong to someone other than Dick is one in 3.3 billion. Bonisteel left Vancouver shortly after the bodies of Dick and Zeschner were found in suburban Richmond in February 1975. His marriage had just broken up and he abandoned his wife and five- week old son. His lawyer James Millar now says Bonisteel was "in a great deal of turmoil" at the time.

On the way to Winnipeg, he raped a woman. Once he reached the city, he raped again. He spent 20 years in jail for the attacks. Prosecutors allege he killed the 14-year-olds who were so close they said they were sisters. Police launched a massive undercover operation to try to get a confession. An investigator posed as the boss of a biker gang in which Bonisteel was desperate to climb the ranks.

The undercover cop told him the police had DNA evidence on him linking him to the murders of Dick and Zeschner. He said Bonisteel had to tell him what happened if he wanted the bike gang to help him make the problem to go away. Bonisteel's lawyer said his client was afraid of the undercover cop who he believed was a ruthless gang leader. Millar said Bonisteel just told him what he wanted to hear.

The undercover officer videotaped a long statement by Bonisteel, who described holding a knife in one girl's chest while the other sat terrified in the front seat of his car. He then sliced the other along her rib cage, "because it was the nastiest thing" he could think of.

Interesting story. I had to read the centrifuge portion twice before I figured out what they were talking about. It sounds as if they were concentrating samples in a speed-vac or with microcon-100's. In the case of the speed vac then yes the samples would all be open at the same time because you can't close them. However, I agree that I would not concentrate suspect and victim samples together. The chances of contamination during this procedure are incredibly remote and I know of no instances of it. Despite this I maintain that I wouldn't do it. It just looks bad even if it really isn't.

As to the experts statement that only " six or seven cells" were in the sample, it sounds a bit unrealistic. That would be approximately 36 to 42 pico grams of DNA. I doubt with extended PCR cycle times and going below threshold you could even obtain a "reliable" partial profile given the age of the sample and the fact the sample has had previous testing, which would decrease the DNA available for current testing. Our labs minimum guide of 200 pico grams, using normal analysis parameters, generally gives a partial profile at best or a weak complete profile.

As to the "contamination" issue. What does sealed mean? A piece of tape on a paper envelope is considered sealed. If that sample spent the entire 20 something years in an unsealed package then they had better have a really good excuse for it or pay the price by a defense reaming. And the glove issue is just simply embarrassing. I never open suspects items while victim items are open. I always change gloves even moving to items from the same individual or even during examination of a single item. We lay our evidence items out on clean butcher paper with new paper for each item. My entire work surface is wiped down with either bleach or RNase between evidence items from different subjects. If I even think for a second I have contaminated my work surface then I will wipe it again prior to opening a new evidence item. Let's just say that I burn through gloves, especially during extraction/clean-up.

I hope that my comments illustrate the point that not all labs are incompetent and we actually do care about what we do. I don't want to wrongly implicate or exclude someone because of sloppy work.

676 quintillion

In the UK, this week, a professor Roy Meadow is being pilloried for criminal abuse of statistics presented in court. Do any forensic statisticians live in the real world ? Multiplying AFs together is just as ridiculous as what Prof Meadow is accused of doing.

http://www.delawareonline.com/apps/pbcs.dll/article? AID=/20050623/NEWS01/506230316/1006

By CHARLOTTE HALE / The News Journal 06/23/2005 <...> But what O'Neill didn't know before a preliminary court hearing Wednesday was how steep the odds are that the DNA belongs to someone else.

Newark police detective Andrew Rubin testified during a preliminary hearing that 18 zeros are needed to create the ratio: one in 676 quintillion. <...>

Self-consistency ?

Who but forensic scientists could make the following reported statements and find a consistent whole ?

"DNA testing of the dried blood last year found it matched another convicted murder, John Ruelas. Ruelas, however, was just 4 years old at the time of the murder and lived in downtown Detroit, a 45-minute drive from the crime scene." "The lab that handled Mixer's evidence also handled Leiterman's DNA and that of the boy, John D. Ruelas, now 40, who is serving time for the beating death of his mother." "He also said there will be highly technical testimony on DNA and that experts will tell jurors that the odds of the samples belonging to a Caucasian male other than Leiterman are less than one in 170 trillion. "

"Prosecutors acknowledged that samples in both Leiterman's and Ruelas' cases were tested at the lab on the same day but have denied claims of evidence contamination. " Sources http://www.courttv.com/trials/leiterman/071305_ctv.html http://www.freep.com/news/mich/mixer13e_20050713.htm http://www.mlive.com/news/aanews/index.ssf?/base/news-13/1121263880267860.xml How dare they present such a dog's breakfast to the court and counter-GIGO fashion expect the court to sort it out. 170 trillion indeed.

So the John Ruelas connection is due to unrelated false match. http://www.mlive.com/news/aanews/index.ssf?/base/news- 13/1121870476251160.xml&coll=2 Wednesday, July 20, 2005 ... Leiterman's attorney, Gary Gabry, has maintained that Leiterman never knew Mixer. and that the two were linked only through questionable DNA evidence. What has yet to be explained is the DNA profile of another man, 40-year-old John Ruelas, was in a spot of blood that was found on Mixer along with Leiterman's DNA profile. Ruelas was 4 years old when Mixer died. He is now in prison for killing his mother in Jackson County.

Sylvia Gill, a DNA analyst with the Virginia-based Bode Technology Group, a private forensic lab, testified that her company was asked by the Michigan State Police crime lab to conduct DNA testing. The results, she said, showed Leiterman's DNA samples matched a partial DNA profile on Mixer's stocking.

Megan Shaffer, an assistant director at ReliageneTechnologiesnear New Orleans, another private company that does DNA testing, testified that the test results of a DNA extract of blood off Mixer's left hand were consistent with those of the MSP crime lab. Shaffer said the DNA tests excluded it from being Mixer's own blood.

Previous testimony in the case showed that MSP lab tests found Ruelas' DNA on Mixer's left hand.

From "millions of trillons more times likely" to zero likelihood

No other scientific discipline is allowed to make such nonsense statements without full account of errors. When are forensic 'scientists' going to start telling the truth in courts of law ? . The true probability is far more like 1 in 20 that any 13 loci DNA profile determination is erroneous. That is the only publically available error rate, from all possible sources of error, for forensic labs blind tested (GEDNAP blind trial concept part 2 ,data for year 2002, pub 2004. No single lab from this validation study or any other inter-lab exercise has published their own results, so this pan-Europe reusult is the only one to go by. Until that error rate is up in the trillions to 1 against then such statements are totally bogus and fallacious.

John Ruelas last week and now the latest pile of nonsense reported here http://www.reflector.com/local/content/news/stories/2005/07/26/20050726GDRlincoln.html ... "inherently lacking the scientific foundation and safeguards required in constitutionally protected criminal trials in North Carolina, especially in the absence of strict assurances designed to stop the SBI lab from repeating past mistakes and reporting erroneous results with little integrity and no consequences to the SBI lab or agents responsible." ... "It's pretty shoddy stuff that's coming out of the lab," Savage said. "They're not doing what anybody would do in what I would call a real lab. If you're going to put someone on death row, put someone in jail for life, or even for a year, at least the science needs to be sound."

I would put it a lot stronger than that.

While laboratory error rates are of significance, no one to date has a reliable way of measuring them. Utilizing one study to base lab error on is both foolish and irresponsible. The statisical significance of an STR profile is, in my opnion, not directly related to lab error rate. I believe it is a go/no-go concept. If there is an error then the STR frequency is irrelevant until the error is identified and understood in the context of a case. The best we can do is develop procedures that allow for the detection of error. Also, the procedures should minimize the chance of error.

So a true probability of 1 in 20 is bogus and fallacious. Do you have some math supporting this? I have read several papers on lab error rate and proposed caluclations to modify STR freqeuncies. All the calculations are based on theoretical lab error rates. However, I still maintain that error rate and STR frequencies are mutually exclusive. I believe lab error rates needlessly attempt reduce the statistical significance of a STR profile. Assuming for a moment that one could accurately measure a labs error rate then the following would be fair: The frequency of occurance for a given profile is "A"; however, the chances the lab obtained that result in errror is "B". Good luck with determining "B" though! Not to mention... what is an error? Please define all categories of error that would be used to generate this calculation.

You hammer away at the statistics we use, yet you are willing to take one study and apply it's results in a broad stroke. This seems inconsistent to me. Shouldn't something be well characterized before application?

Delighted to explain. If you are aware of any other inter-lab validation test conducted in blind fashion please tell me. I don't mean internal validation checks as in these terms that is meaningless as using same reagents/machines etc The relevant table of results from the only proper published study I am aware I've placed (fair-use fashion ) on http://www.nutteing2.50megs.com/gednap.gif ( if remote linking to an image does not work it is on a link about 1/2 way down on the URL in sig piece)

It shows 0.4 per cent error rate in 30,479 single locus tests. Combined results from 136 labs in 30 European countries and multi-locus tests across 18 autosomal STRs and 12 Y-STRs. published in International Journal of Legal Medicine (2004 ) 118: p83-89 http://www.springerlink.com/app/home/contribution.asp?wasp=df08a8b230994088a1e8983c28228a00&referrer=parent&backto=issue,4,13;journal,10,54;linkingpublicationresults,1:101167,1 or http://tinyurl.com/cnquy The GEDNAP blind trial concept part 2. This data is anonymised so the good and bad are lumped together - considering the bad do not know they are bad (or at best, in disagreement with the consensus).

Only one error per profile on one locus (1 or both alleles) is sufficient to invalidate a profile. Simple maths 0.4 *13 = 5.2 per cent or 1 in 19 , say 1 in 20 for Codis , 1 in 25 for NDNAD structure

Until more such proper inter-lab validation studies are undertaken and published this is the only series and the only data to work with. We can quibble about 1 locus per profile or 5 per profile or whatever but this report didn't divulge. I can come back by mentioning that the stains were, forensically almost unheard of, 50/50 blood/blood stains. It is still an extremely long way short of 1 in trillions error rate. If practising forensic scientists have not obtained and read this report and others on false homozygosiies etc then shame on them.

All labs say they are error free , because they just don't know otherwise until such blind exercises are undertaken. Then surprise - surprise the bad ones in this GEDNAP process were informed but has anyone seen them mention their indidual results - NO.

No links to other relevant inter-lab validation studies heard. So until there is then this Gednap is the best available, don't blame me, I can only use what is available. There was qualitive analysis of the errors discovered but no quantitive breakdown of the "0.4%" figure. Error types Sample transposition Transcription errors Previous studies showed marked errors from certain types of stain so surprise,surprise they settled on the least error prone of fresh blood source only. Wrong interpretation of minor allele and stutters. FGA (42.2) often unrecognised Problem distinguishing THO 8.3,9,9.3 and 10

They had deliberately used the rare FGA (42.2) but there was no mention of deliberately including homozygous pairs known to produce false homozygous results. Separate study on this showed FSI 143 (2004) 47-52 Same sources processed on SGM plus and Powerplex and compared. 15 errors in 2055 single contributor profiles not otherwise selected to have the following error-prone alleles, so error rate from these otherwise not distinctive or rare loci/allele combinations of 0.7 per cent or 1 in 140
vWA SGM+ Powerplex16
1 15,15 15,17
2 17,17 17,18
3 15,15 15,18
4 16,16 16,18
5 18,18 18,21
D8S1179
6 12,12 12,16
7 14,14 10,14
8 13,13 13,18
FGA
9 22,25 25,25
10 23,23 21,23
D18S51
11 14,16 14,14
12 10,10 10,18
13 15,16 15,15
D5S818 comparing Profiler and Powerplex
14 10,11 11,11
145 10,12 12,12


Please inform me how many labs cross-check for this source of error by repeating on other systems ? False homozygosity is a systemic failing so I cannot see how error rates can be better than 1 in 140 so sets that bound.

I come from a proper trained scientific background and I keep seeing statements in courts where it is patently obvious that the people speaking have no proper scientific training. Yesterday I saw reference to 3.482 billion and last week reference to 171 trillion. As always there was no mention of the degree of error in these figures. My training says that if a number is given as the result of any processing then if no error bound is given then it is implied by the degree of precision in the stated numbers. The result cannot have a greater degree of precision than the error in the most influential input factor/s. So 3.482 billion is implied to be accurate to the nearest 2 million or even 1 million. 171 trillion is accurate to the nearest trillion, all utter tripe. It is just as grating to the ears of a proper scientist as seeing someone using a calculator and pronouncing that some result is 2.34278547 where even quoting 2.3 would be overstating the precision.

That is before bringing in the matter of the square law of false matches once the threshold has been reached. By the time you got to a billion profiles let alone a trillion there would be millions of unrelated pair matches let alone triples, quadruple matches etc. With no way of predicting whether this defendent's profile would be one of those false matches.

I use Identifiler and our validation and everyday use shows absolutely no evidence of false heterozygosity. Also, "best available" isn't always the best or even the most useful.

False heterozygosity is not the problem - it is false HOMOzygosity that is the irremoveable 'error' that puts an upper bound on error rates.

I found no reference to Identifier being immune to false homozygosities. How often do you run a sample both through Identifier and say Powerplex 16 which both analyse the 5 loci shown to be prone to FH. ?

I was trying to be charitable but the "best available" in my terms would have ben the results for Gednap 20 & 21 year 200 which show 0.7 per cent error rate or 1 in 12 . After that result they moved the goal posts. They dropped the stains such as "cigarette butts and mixtures of body fluids as well as hairs". Because these samples were producing disproportionately more errors. Beggars belief doesn't it - just what is forensically more likely than 50/50 blood/blood traces. So I'll revise the so far proven situation to 1 in 11 profiles being erroneous.

If errors are so rampant how can there be any "known homozygotes" or "known" anythings? All must be tested by lab personnel at one point or another - thereby inciting more error.

How can a known homozygote give false homozygous results? Wouldn't a known homozygote have homozygous results?

AFAIK it is an intractable systemic failing that cannot be overcome by normal single kit analysis. Full explanation of biological reasons are in the full text of which the abstract is http://tinyurl.com/75dbu They undertook further biological research but full textual results/explanations hedged with a lot of "appears"/"appeared to be" Discrepencies on vWA (apparently) due to mutation upstream of the repetitions D8 " " downstream of the repeats FGA " " downstream of repetition D5 " " downstream of repetition D18 mutation Pointers to other published False Homozygosity results for D16 and TPOX

Allelic dropout "due to stochastic effects was also eliminated" The D5 electrophoregram is included and it is not a matter of mis-interpretation. There is not the slightest trace above mush level on Powerplex16 for the '10' trace of D5(10,11) and D5(10,12) shown on Profiler +

As far as I can see this 15 in 2055 or 1 in 140 represents the limit of error for single kit processing, even if absolutely all human error, mis-interprertation etc could be removed. The 2055 subjects in the study were not pre-selected so can be considered generally representative of human populations.

The most simple response to false HOMOzygosity is... SO WHAT?

Missing alleles just means my stats aren't going to be as good. It will never cause me to include someone incorrectly. So I would dispute it as even being a relevant "error". As far as mixtures go, I routinely see allelic dropout in my casework; at least what I perceive as dropout based on camparison to references. Based on your "error" any incomplete profile or mixture profiles are errors. News flash... these are not errors. Incomplete profiles are what they are.

False homozygosity can have some impact on databases in that the presence of an additional allele has to be resolved in the case of a preliminary match. However, we have not encountered this problem at our lab. I am sure it will eventually happen.

When alleles start to "drop-in" then we have a problem. It is known as contamination. The reverse is not true though. So you can't take false homozygosity rates and modify statistics given the fact that they aren't errors. The "missing" allele has already altered the stats.

Excuse my ignorance, but could someone shed some light on 'false homozygosity'?

Is it a missing allele in a profile? If so, would it really be labeled homozygous?

Is it an error that makes a homozygote out of a heterozygote?

So ,hypothetically, you have an electrophoregram in front of you ,it is a profile from a single individual contributor,clean and uncontaminated and it shows one peak corresponding to vWA 15. No doubt about it just a single peak, perfectly on ladder. This person , unknown to you, tested on another company's system shows two peaks, for vWA (15,17). By what incredible insight do you ascribe vWA (15,17) rather than vWA(15,15) to that single peak on your normal single system/kit analysis?

"we have not encountered this problem at our lab" - have you even looked? , have you tried divided samples on 2 or more systems and actually compared results ?

The "so what" is it puts an unassailable bound on DNA profile accuracy in normal single kit use.

I still have not heard properly constituted rebuttal evidence against the upper and lower bounds for DNA profiles. That is, until proven otherwise, between 1 in 11 and 1 in 140 for CODIS and 1 in 14 to 1 in 140 for FSS/NDNAD.

False homozygosity is when at a particular loci you only see one allele when in fact there should be two alleles (heterozygosity). It can result from a bad amplification, a mutation in the primer binding site at one allele, or from a mosaic between tissues (I actually know of someone who has this). Regardless, false homozygosity is rare. If it is consistent due to a primer binding site mutation or mosaic condition then the result will be present in any forensic unknown samples and the reference. The analyst will be ignorant of the "error". The chances of a false inclusion due to this phenomenom would be extemely small.

My reply is that I don't care. It can happen. I can't change it. I would love to see the RFU levels of the profile in which the 17 was absent. The bottom line is that this occurance is rare and as long as the 17 is absent in every sample then it doesn't effect my interpretation of a match.

The FSI 143 (2004) 47-52 report only has plots for the D5 '11,11' and '12,12' Powerplex plots that showed (10,11) and (10,12) on Profile, no RFU levels . Citations in that article give further FH results by other workers so not one isolated study : J. For. Sc. 46 (2001) p637-641 also shows FH of 0.2 per cent for FGA " " " 43 (1998) 1103-1104 shows D16 and TPOX FH http://journalsip.astm.org/JOURNALS/FORENSIC/jofs_toclist.html shows vol/year agreement to these refs but I cannot find the cited articles/abstracts there.

You have not given rebuttal evidence , just a qualative counter assessment. 3 quantitive studies to me, 0 studies to you is not rebuttal. Where is your data for the upper and lower error bounds for single-kit DNA profiles ?

Qualatative is all that is needed and there are no error bounds for the kits that I know of.

As far as I am aware Profiler, Cofiler, Identifiler, GenePrint and PowerPlex are all compliant with the CODIS requirements and results submitted for storage on Codis. These are not mutually consistent as far as false homozygosity (FH) is concerned. It is outrageous that the FH inconsitencies , hence intractable systemic errors, are not determined published and presented in courts.

On the more general theme of errors (human included) I now see that the latest published Gednap report is on the web rather than locked away as expensive subscription access in Int J Leg Med (2004) 111:83-83 http://medweb.uni-muenster.de/institute/remed/spurenkommission/Information/IJLM_GEDNAP_II.pdf

Gednap 24/25 fudged to bring the per locus error rate down from the 0.7 per cent of the earlier Gednap 20 validation trial

http://medweb.uni-muenster.de/institute/remed/spurenkommission/Information/Manual_englisch07_04.pdf
....
GEDNAP 20 the following samples wereprepared:GEDNAP 201. 
Person A: 25Ál blood (female) on cotton cloth2. 
Person B: 25Ál blood (male) on cotton cloth3. 
Person C: 25Ál blood (male) cotton cloth
4. Stain 1: unsmoked filter cigarette with 10Ál saliva
5. Stain 2: 25Ál blood mixture (Persons A:B, mixed 1:2 v/v)
6. Stain 3: 25Ál blood mixture (Persons A:C, mixed 3:1 v/v)
7. Stain 4: Buccal swab from Person A
...
Being the previous criteria, now downgraded to 50/50 blood mixed stains only, no cigarettes etc, to bring the per locus error rate down from 0.7 to 0.4. Despite being a "blind trial" the stains were mixtures of persons A,B and C, known, in these outline terms, to the participants. The full protocols for Gednap 24 to 27 are not available to the public AFAIK (rat smelling time - cf concurrent thread on this group about "ASCLD-LAB accreditation" ).

They were rigorous enough to include THO 9.3 & 10 and FGA 42.2 (perceived as trip-up ones by some ) but if I was running the tests I would make sure a few False Homozygous prone alleles were included eg from pool of the vWA,D8,FGA,D18 or D5 ones mentioned in FSI 134 (2004) 47-52

Outcry as charges dropped in rape case despite DNA link

I reckon I know why - anyone else care to speculate? http://news.scotsman.com/scotland.cfm?id=1738622005 Sat 6 Aug 2005 Outcry as charges dropped in rape case despite DNA link NICOLA STOW CRIME REPORTER A MAN charged with raping an Edinburgh schoolgirl after a DNA test linked him to the alleged attack 13 years ago has been told the case against him has been dropped.

Police charged Iain Orr, 33, with the offence in June last year after he was arrested for another minor non-sexual assault and provided a mouth-swab sample.

But the procurator fiscal has decided it is "not in the public interest" to proceed with the rape case, and has refused to explain why. Politicians today demanded an explanation be given for why the case was dropped, saying that the public had a right to know.

Analysis of the DNA swab taken from Orr using the national database, found a direct match with the alleged rape of the 15-year-old girl in a common stairwell at the top of Leith Walk back in 1992. Orr, understood to be a contractor from the Drumbrae area of the city, was unaware his DNA had been stored on the database until his arrest last year.

Samples taken from the crime scene at the time were not put into the national database until six years after the alleged rape, during a "cold case" review by police and forensic scientists. Police arrested the man after the results of the extensive DNA search came back in June last year with a positive match.

A report was then sent to the procurator fiscal but no further action is to be taken. A Crown Office spokesman said: "After examining the case, the fiscal has decided it is not in the public interest to proceed with this in court." Neither the Crown Office or the police would say why the case had been dropped.

However, politicians today criticised the decision. SNP justice spokesman, Kenny MacAskill, said: "Maybe there is a good reason why the fiscal decided not to proceed with this case. However, the fiscal also has a duty to satisfy the public and they are entitled to know why.

"After all, most people would expect this crime to be pursued rigorously no matter what the passage of time, irrespective of whether this man is currently serving a sentence. This should not be a difficult case to prosecute - DNA is usually bang-on." Despite extensive police inquiries at the time, no-one was arrested for the alleged rape of the teenager in the summer of 1992.

It was alleged the youngster was attacked in the stair of a block of flats in Elm Row on July 20. DNA was taken from the scene, but no means existed at the time to carry out extensive searches based on DNA samples. It wasn't until 1995 that a national DNA database was set up and samples taken from arrested males began to be collected at police stations across the country as a matter of course.

The database has DNA samples from across Scotland, but can also be linked into the UK system. Three years later - and six years after the attack - forensic scientists took the sample and put it on the DNA database as part of a wide-reaching cold cases review.

Mr Orr's arrest after a nightclub brawl in August 2003, and the subsequent routine sample taken from him, was enough at the time for police to link him to the alleged rape 12 years before. A Lothian and Borders Police spokeswoman today said the force was unable to comment on the fiscal's decision.

Scottish Tory justice spokeswoman Annabel Goldie said she could not comment on individual cases, but added: "The fiscal may have very good reason for making this decision, it is important for public confidence that the reasons for not proceeding with prosecution are made clear."

Wait a minute--If he was "unaware that his DNA had been stored on the database until his arrest last year" , how did the authorities get his DNA in the first place? There's no mention that his DNA would have been in their database other than the fact that he left it at the scene of a rape. Perhaps those who are worried about possible misappropriation of their genetic material should be a little more careful about where they deposit it.

I would have expected far more precision on this group. "HIS" DNA has not been found anywhere.

A set of numbers that may reflect the biology of a miniscule subset of his DNA has been matched via a computer database to the same set of numbers derived from a crime scene sample stored, more than likely in less than ideal circumstances, which may or may not reflect a miniscule subset of SOMEONE'S DNA left at a crime scene 13 years previously and analysed many years later.

Your concern over the naming of Iain Orr would be laudable if you were consistent, but you are not. Orr may or may not be innocent of the 1992 rape. We do not know and probably never will.

I notice that at no point in your diatribe do you mention the work of the Innocence Project. They have cleared many wrongly accused people by using DNA testing to demonstrate their innocence. Do you question their innocence? They were named and to some extent will always be idfentified with offences that they DID NOT commit. Where is your outrage on their behalf?

Two years ago I detailed the case of the Cardiff Five - remember them - (Yusef Abdullahi, Steve Miller and Tony Paris were convicted and the cousins John and Ronnie Actie were acquitted) on this list. They ARE undoubtedly innocent. They were wrongfully convicted in 1990 and the three freed in 1992. In 2003 following an excellent reinvestigation involving DNA evidence the real murderer Jeffrey Gafoor was caught and convicted. Confronted with IRREFUTABLE DNA evidence Gafoor pleaded guilty and apologised both to those wrongfully accused and to the victim Lynette White's family.

The Cardiff Five ARE UNDOUBTEDLY innocent. DNA evidence not only conclusively eliminated them, it resulted in identifying the REAL murderer. Funny how you are so full of indignation over Orr, who may or may not be innocent, but your silence on those who ARE innocent because DNA proved it is deafening. For the record I would prefer annonymity of suspects as in my opinion it is a prerequisite to being presumed innocent, but unlike you I apply it to everyone INCLUDING those whom DNA has subsequently proved innocent.

Despite the real murderer pleading guilty and apologising in the Lynette White Inquiry there are still some who believe no matter what that they are guilty. Where is your indignation and outrage over this? Perhaps in your world the fact that DNA proved their innocence by proving the guilt of the real murderer makes them less deserving of your outrage. Ill-informed nonsense regarding the DNA evidence in that case fuels the outrageous belief that despite DNA profiling proving their innocence they are somehow guilty. They are not. DNA testing cleared them unequivocally and identified the real murderer. Deal with it!

I'm struggling with the logic here. Whether the victim's identity is known to relatives etc or not makes no difference to the Fiscal's disclosure. If relatives don't know then that is still the case after disclosure. If relatives do know her identity then they may be pressurising her to assist prosecution now the background has had media coverage. That makes no difference whether the Fiscal discloses or not, the relatives in the know would know of her non-assistance or at least surmise this is the reason. After all it cannot be failings in the DNA business as 99.9.?. percent, whatever of the population, know that a DNA match is the closest you are going to get to guilt.

My "diatribe" is quite long enough as it is without adding a whole new area that has been well covered by many others and has had plenty of conventional media coverage. There is no problem, practical or conceptual, with using DNA to exonerate, it is inclusions from large database trawls and false matches is my particular concern. An odd error due to deemed spontaneous mutation or whatever is no problem for excluding from a small pool of otherwise implicated possible perpetrators. False inclusion with or without processing errors is just too high a probability now there are millions of profiles in databases. As there has been no peer-reviewed validation study on modern day analysis of historic crime scene DNA samples there could well be false exclusions/exonerations but I will leave that to you to research. The results of that study would be applicable both ways, historic false inclusions and false exclusions. I can only name one other person in the world who is exploring down similar lines as myself and he has not been able to put figures to false match likelihoods and overall DNA profile analysis error rates.

I don't expect it to do much good, but it kind of annoys me that he is so closed-minded about DNA testing It seems to me that it's good to have gadflies and watchdogs, even if we dislike their position or degree of obsession. Even if they're partly or wholly in error. That's what keeps the field accountable. That's how junk science and fraudulence have been exposed. Such people at least make us take stock of our positions and think through our own logic and proof. After that, we can just ignore them, but I'm all for having those voices in our midst. Conspiracy theories do serve at least one useful purpose, they regularly expose morons (among the public, the media, and politicians). I don't know about the UK, but in the U.S. the people have no "right to know", the press is free constitutionally, and they and the people have the "right to try and find out".

Gafoor was identified following an investigation of the National DNA Database. Investigation of particular alleles within the DNA profile of the murderer resulted in police identifying the family of the real murderer. One allele alone eliminated 99% of those on the database. Searches at eight and twelve eliminated many more. Applying this geographically resulted in one profile on the database standing out. He was a nephew of the real murderer Jeffrey Gafoor.

Gafoor voluntarily gave a buccal swab to poilce. He then attempted to commit suicide by overdosing on paracetomol. Police knocked his door in - they put him under surveillance due to his attempt to explain his DNA being found in the flat in advance of the test results by saying he had had sex with her. The DNA had come from blood.

Police tested samples taken during the original inquiry. This included items that were known to have the murderer's blood on them and also items that had been taken in 1988 but not tested then. Both the previously tested items and ones that had not been tested before had DNA that bbelonged to a man who was directly involved in the murder.

Furthermore a scientist was able to reconstruct the exit route of the murderer from the flat by blindfolding himself in exiting the flat. Every place he touched was noted and tested. Full DNA profiles that matched those obtained from the other items were obtained. As with a drop of blood that was recovered from between the wall and skirting-board and two layers of paint - the flat was decorated as a health hazard in 1988 - the profile obtained matched the others.

Gafoor appears to have no problem acknowledging his guilt meaning the way he was unmasked as Lynette's murderer involved validated techniques. I cannot understand why you have such a problem with it. There really is no doubt that Gafoor is guilty and that the original defendants were and are wholly innocent. Without advances in DNA testing Gafoor would never have been identified as Lynette's murderer and the Cardiff Five would still be enduring a thoroughly unjustified and whispering campaign. Without Gafoor's conviction there would still be people claiming they are guilty and got out on a technicality. Thanks to DNA testing anyone who still says that is an irredeemable moron!

I can see both sides but: I can see why there would be non disclosure if due to a DNA profile failing. I cannot see what difference, to any pressurising on the victim by relatives, that otherwise anonymous official disclosure as the reason, could make on her. Any damage to the victim has been done by disclosure in the media of the re-opening and theoretical closure of the crime. Until there is official disclosure then it is open to any interpretation - its just that most people would take your view and be totally unaware of any other possiblity.

Why are the same problems not apparent in using DNA to exonerate as they are to prosecute? Can the same errors not be made only in opposite (i.e. instead of false matching, false exclusion)? If the DNA process is so faulty, why should it be used in any way?

By the way, there are numerous reasons why the case would be dropped - not all of them have to do either with the victim herself or the DNA evidence. For instance, there could be a break in the chain of custody; there could be evidence that was improperly collected and/or stored, there could be not enough evidence besides the DNA to prosecute, there could be any number of mundane legal reasons why the charges were dropped. Jumping to conclusions, while it is easy, generally does not generate the appropriate answer.

Alleged Falsified DNA Test Results

Army Civilian Suspected in DNA Deceit By ROBERT BURNS, AP Military Writer

WASHINGTON - The Army is investigating allegations that a civilian forensic examiner at the Army Criminal Investigation Laboratory at Fort Gillem, Ga., falsified DNA test results. The allegations, if true, would throw into doubt hundreds of criminal cases dating back at least a decade.

The examiner on June 2 admitted to making a false entry on a control sample used during one DNA examination, and the laboratory is now reviewing 479 or more cases the accused examiner has worked on since he began in 1995, according to an announcement Friday by the Army Criminal Investigation Command, or CID. The examiner was suspended from duty in May after the allegations surfaced. His name was not released.

The Gillem lab is now reviewing all cases that the unidentified examiner handled, including an unspecified number that led to criminal convictions, officials said. The top lawyers of the Army, Air Force, Navy and Marine Corps have been notified by letter of the "identified deficiencies" in the DNA testing. Also, the CID is alerting all Pentagon criminal investigation organizations so that custodians of evidence from cases that the accused examiner handled can preserve that evidence.

The lab at Fort Gillem is the only Army facility that performs forensic examinations in support of military criminal cases. It provides services to all military investigative agencies and is the only accredited full-service crime lab in the federal government outside the FBI. This was not the first indication of potential problems at Fort Gillem. The examiner now under investigation was temporarily suspended from DNA case work in January 2004 when contamination was detected in his testing process, officials said. After "remedial action and retraining" he was returned to work in September 2004.

No other details of the earlier suspension were released Friday. "We are taking every step necessary to ensure we have an independent, impartial review of the issues at hand," said Chris Grey, a CID spokesman. "At this time the incident appears to be isolated to one individual examiner, but we want to take very step necessary to make certain that is the case."

The CID investigation is being led by the command's Standards of Conduct Office, and the Pentagon's inspector general has been asked to conduct an independent review of the CID probe once it has been completed.


Email Paul Nutteing by removing 4 of the 5 dots
or email Paul Nutteing ,remove all but one dot
Or a message on usenet group uk.legal has got to me recently a couple of times.
A simulation of a large DNA profile database
A simulation of DNA profile 'families'
A simulation of DNA profile families with consanguinity
A simulation of DNA profile 'families' for 6 generations
dnas.htm revisited with all alleles represented
dnas.htm revisited for >8 percent allele frequency subset (similar ancestry )
Simulation of Taiwanese Tao and Rukai populations to explore the effect of within and without ancestral clusters
Basques autochthonous DNA profiles simulation, 9 loci
Australian Capital Caucasian 9 loci simulation
Australian Capital Caucasian 9 loci simulation, >= 5% allele frequency
CODIS, 13 Loci Caucasian Simulation
Automating the macros
Otner match scenarios
'Peer review' of some of the dnapr.htm material
Continuation of sparring on http://groups.yahoo.com/group/forensic-science/messages with forensic 'scientists' using my pseudonym of Nona Revers or nonarevers
'Peer review' of some of the dnapr.htm material , part3


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