Mr. Sims, you discussed yesterday a study by the Federal Bureau of Investigation concerning efforts to induce cross-contamination in the handling of samples?
I think at one point you talked about how this FBI study, they had FBI agents coughing over samples?
Well, I don't know that they were FBI agents. I think they were actually laboratory people that were not necessarily agents, but yes.
Well, I--I believe that work was done mainly by Dr. Comey who is an employee of the FBI, and I think it was a woman by the name of Pamela Fish who I believe is with the Chicago Police Department. I think those are the two that did those experiments.
Now, is there--to your knowledge there is no such thing as a standardized cough by either FBI employees or employees of the Chicago Police Department?
And a sneeze is more likely--forgive my bringing up the details of this, but to--to give you an effluent or a spray than a cough?
To my knowledge I don't recall that being in the table, no. I think it was more of a cough.
And they did find that saliva, mixed with blood, that actually the amount of DNA that you will get from the saliva mixture is two times the amount that you would get from the blood?
I don't recall it being two times, but yes, the saliva could make a big contribution.
And scientifically that makes sense to you, doesn't it, because saliva, in terms of its volume, has a higher concentration of DNA than blood?
Well, I think saliva can have a lot of DNA in it because of the cells that line the mouth, but there is a tremendous variation, just as there is from cough to cough, from spit to spit.
Well, in general, no matter who--if you compare somebody's spit to somebody's blood, right, in equal volumes, you are going to find more DNA in the spit than the blood?
And just to illustrate it, the kind of things you do in the laboratory, there is something called a centrifuge?
And what would happen is that the cellular material would go to the bottom of the tube?
Well, the red cells tend to sediment and then the white cells tend to form a layer on top.
And then there is a thin film that I think people in your line of work call a buffy coat?
Right. They are different from the ones that would be on your epidermis, for example.
Right. And the epithelial cells that you get from the saliva, if you looked at the bottom of the test-tube, that would be what you would see at the bottom?
And so if you were to just take a volume of blood and a volume of saliva, typically, right?
You look at that buffy coat which would be the amount of the white cells or the amount of DNA you could get out of that volume of blood, right?
And typically compare it to the other two where you would have the cells from--the epithelial cells from the saliva, right?
In the same volumes, you would expect to see more DNA from the epithelia cells than the saliva, typically?
Well, the problem with--with saliva is it is not like blood. Blood tends to be more typical in that when you draw it out of the arm, people's blood tend to all look alike. Their DNA might vary, but they tend to look alike. But saliva varies because we take saliva from suspects and victims in sexual assault cases, so you look at these things and you see a lot of variations, but there can be--to make this short, there can be a significant amount of epithelial cells in saliva.
--you would be more likely to find epithelial cells from the effluent of a sneeze, wouldn't you, than a cough?
Well, if--if--I mean, you have to remember some people, when they cough, they really hack a lot, and so they may be producing a lot of phlegm.
Well, all right. Well, let's--getting to the bottom line here, in terms of this FBI study, you think it might have been a reasonable idea, instead of having some undefined kind of coughing, to have somebody sneeze?
--talking again about the FBI study, bottom line here, the samples involved in that study, right, the--the samples that they were looking at in terms of trying to see whether they were cross-contamination did not involve degraded samples, did it?
And the discussion that we have been having here has to do with the possibility of cross-contamination of one set of samples that are degraded?
And you were asked is it your opinion that a typing error in the from process is more likely to result in a false exclusion than an inclusion?
And I take it that your answer was based on your experience in forensic DNA typing?
And when you are doing forensic DNA typing, typically that involves a case where you will get a result, a DNA result, and then it will be introduced in court with respect--and maybe against somebody who is accused?
It can happen. But when it is being used for purposes of incrimination, it is used for--let's put it this way: Talking about false positives and false negatives?
There are many situations where you will have what we would characterize as a positive result, that is, there is a consistency between DNA typing found on some sample and a person that is accused and that would be called, let's say, a, quote, positive result?
And you had that in mind when you are answering the false positive question yesterday?
Now, in a--when you are using PCR typing for purposes of making a diagnosis in a clinical test--
You were asked yesterday in this connection about--you made reference to an article by Mr.--Dr. Sensabaugh concerning, umm, false positive rates and PCR typing?
Objection. That misstates the testimony. There was no such testimony on rates, your Honor.
Do you know what the false positive rates are for PCR typing in clinical medicine?
Do you know--you were asked questions comparing forensic typing in DNA typing in forensics and clinical medicine yesterday by Mr. Harmon?
All right. And let's just talk about what you do know with respect to the use of forensic typing in clinical medicine.
Do you know if PCR typing in clinical medicine is used to do a diagnosis of, let's say, some--you know what a pap smear is?
All right. A situation where you--an analysis might be done on a pap smear to see whether or not somebody might have a tumor that is either malignant or benign?
In--when PCR typing is used as a screening device in clinical medicine, do you know if it is used in situations to make an assessment as to whether or not somebody, umm--where you will make a prediction based on the typing result as to whether or not somebody has, let's say, a certain genetic disease?
Do you know if in clinical medicine, using PCR typing, one can make a comparison of what the DNA typing result is and compare it later to whether or not the typing result accurately predicted the outcome?
In a--using forensic DNA typing in the context of a criminal case, the only way that you can find out if you had a false positive is if some other evidence emerges afterwards which would indicate that the DNA typing was incorrect?
And in the first round of CACLD studies two laboratories, cellmark, forensic sciences associates, got false positives?
Uh-huh. And the information that you have read about that study, do you rely upon it?
Have you relied upon it in forming your opinion about the reliability of forensic DNA typing?
I know, for example, that Dr. Blake mentioned it in the case work article, the experience he had and why it was better--why he found it was better to shift to the reverse dot-blot.
Excuse me. The only question is what have you read with regards to the CACLD study? Dr. Blake's article. We have established that.
I think--I think there is a mention of the CACLD study in the NRC report and I think there is a mention of it in I recall reading something about it I think in Dr. Thompson's article.
Uh-huh. In what you've read, would you rely upon these articles that you've read in terms of their accuracy in reporting what occurred in the CACLD study.
Excuse me, counsel. The way you are phrasing the question, it is never going to work.
I guess so. This doesn't look particularly fruitful here. The jury has already heard about the CACLD study and has also heard testimony from cellmark.
To your knowledge, in proficiency tests performed by the CACLD, were there more false positives than false negatives?
Well, in conventional serology I--I actually started doing conventional serology back in 1976, so I guess I did that for about fourteen years, something like that.
And I believe you have told us that--well, withdrawn. And the EAP system looks at enzymes within the red blood cells?
And forensic DNA testing with DQ-Alpha or polymarkers would be looking at nucleated cells, correct?
And I think you have already told us that in terms of blood, only one percent of blood contains the white cells that has the nuclear DNA?
Something like that. I know that figure a little differently from my knowledge, but it is on that order.
Blood is mostly red cells, that is the point, and very few white cells by comparison.
When you opened the package--packages that contained the fingernail scrapings--you received the packages that contained the fingernail scrapings and the clippings?
And at that time you were aware that Mr. Matheson had conducted EAP testing and conventional serology testing on scrapings?
And after looking at those packages, did you then close them up without conducting any testing on them and send them back to LAPD?
And did you have any discussions with Mr. Matheson after you closed up the packages?
I think I did. I'm not positive of that, but I think I did talk to Mr. Matheson about the fingernail scrapings.
Well, Mr. Sims, have--are you aware of literature that documents a degradation pattern for the EAP system?
And in that literature have you ever--in that literature is there any degradation pattern that shows that a BA can degrade into a two-banded b pattern?
Most of the literature that I am familiar with talks about what generally happens, although I do recall reading in the literature a citation for I think it was in the--one of the British laboratories where they saw a BA being mistyped as a B, and that--I have seen that in the literature. Not as part of a study, but as some--an observation.
Have you seen in the literature any documentation of a degradation pattern where a BA degrades into a two-banded b pattern?
I--I don't recall seeing that, unless there may have been something in one of Dr. Grunbaum's papers, but I can't cite it offhand.
And Dr. Sensabaugh is the person that has done, would you agree, the most extensive work in examining the EAP system?
And in his published articles have you ever seen anything that documents a degradation pattern where a BA degrades into a two-banded b pattern? Anything he has written?
In your own experience, in all the years that you have performed conventional serology, have you ever seen a BA degrade into a two-banded b pattern?
Well, the problem with the EAP marker--I mean, I can recall generating a lot of inconclusive results with EAP, because it can be a difficult marker, but--
Well, I think--I think in order to do that you have to be assured of what the type is to begin with, if you understand what I'm saying. In other words, if I have a stain, I have to be sure of the type to begin with. You would have to do it as a research project.
Mr. Sims, I'm just talking about your experience now in typing. Have you personally ever seen a BA degrade into a two-banded b pattern? Have you ever seen that? Yes or no?
Now--your Honor, I'm going to start this, but it is going to take more than ten minutes.
Now, Mr. Sims, in the PCR amplification process, whether you are using the DQ-Alpha system, the polymarker system or the D1S80 system, in terms of basic principles, would it be fair to say that what is happening is one is starting with a certain amount of genetic material?
And then what happens is that in the PCR amplification process itself there is a--what are known as cycles?
Could you explain that for us, how that works and how a piece of starting material, umm, is amplified up into many larger fragments? Many more fragments, I'm sorry?
More fragments, right; not larger. The--this is the PCR process, and I won't go into great detail with this, but what you are doing is you are starting with a certain amount of what we call template DNA. In other words, that is the DNA that you extracted from the stain. And then you are doing what is called amplifying a particular segment of that DNA, a very small, relatively small portion of that DNA, and you are using that then to--that repetitive or--or you are making additional copies of a particular area, then you are making copies from copies and copies from copies and so on and so on. And that is why you see what we call this expedential expansion of the number of fragments that you get.
Now, let us assume that the starting material here, all right, contains DNA for--let's pick the DQ-Alpha system, all right?
All right. Let's assume, for purposes of this, that in this starting material we are talking about DNA that has the genotype 1.3, 1.3 for the DQ-Alpha system.
So in other words, would it be pair to say that when you begin making the copies from that starting material that with each different cycle you are producing more and more fragments that are about, what, 269 base pairs long?
And as the cycles go on, you are producing--what is this number at the end, after 32 cycles?
And when you do that amplification on one of these little microfuge tubes, after you put it in that thermocycler machine, you are going to get inside that tube 4 billion 290 million fragments of 1.3?
Well, again it depends on your starting material, but that is the idea. That is proper.
And a single amplification could contain something on the order of a trillion copies of an amplified target sequence?
I don't think at our levels that we get up to a trillion copies. I think maybe a billion is sort of the neighborhood.
A billion copies. When we talk about the amplified target sequence here, we are talking about that 1.3?
Well, no, it is not really a staggering number of molecules, I mean, if you look at the air, think how many molecules are in the air, and that sort of thing. It is not a staggering number of molecules; it is just a large number.
KEY QUOTEWell, it is enough to cover many square miles of land if you just took them out of the tube and spread them out?
Maybe in a string or something like that, I suppose there could be something like that, yes.
And with the contents of that reaction with these 4 billion 290 million fragments, it is certainly, if it got out of that tube, could cover a lot of square footage in a laboratory?
And in a DNA laboratory, when you are doing these PCR tests, you are amplifying up in the tubes these billions of fragments again and again and again?
Well, you are--for example, if you did several samples, yes, each tube would contain those--that large number of fragments, yes.
And if some of these fragments--are these fragments one of these fragments, is it visible to the naked eye?
You couldn't see it. You would--you couldn't see it. I mean, it is extremely tiny. I mean we are talking about things on the atomic--well, it is not an atom obviously, but several atoms. You can't see it.
When you said it is visible to the naked eye, are you talking about seeing it under the microscope?
With that, not being able to visibly see it, your Honor, we will move on.
KEY QUOTEAll right. Ladies and gentlemen, we will take a brief ten-minute recess. Please remember all of my admonitions. Don't discuss the case amongst yourselves, don't form any opinions about the case, don't conduct any deliberations until the matter has been submitted to you. Also, do not allow anybody to communicate with you with regard to the case. As far as the jury is concerned, we will stand in recess until nine o'clock. All right. Mr. Sims, you can step down. Monday morning, 8:45.
It looks like you've got 4 billion 290 million fragments.
it is not really a staggering number of molecules, I mean, if you look at the air, think how many molecules are in the air... It is not a staggering number of molecules; it is just a large number.
No, I can't recall seeing that.
The jury has already heard about the CACLD study and has also heard testimony from cellmark. So let's proceed.
With that, not being able to visibly see it, your Honor, we will move on.