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.
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
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
....
GEDNAP 20 the following samples wereprepared:GEDNAP 201.
Person A: 25µl blood (female) on cotton cloth2.
Person B: 25µl blood (male) on cotton cloth3.
Person C: 25µl blood (male) cotton cloth
4. Stain 1: unsmoked filter cigarette with 10µl saliva
5. Stain 2: 25µl blood mixture (Persons A:B, mixed 1:2 v/v)
6. Stain 3: 25µl 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.
