Mr. Sims, what is total number of items, including substrate controls, that your lab tested in any way?
This would be the number of items that we actually extracted. Something like 108 samples, including the substrate controls.
Okay. And--rather than go item by item on what was conserved, to speed things up, can you tell us of those items, how many of those items were actually totally consumed in the testing?
Yes, I can tell you that. I need a moment to count, but I can tell you that fairly quick.
The items that--these are the ones where we consumed the sample. This would be item no. 113, which relates to a hair.
These are LAPD numbers. Okay. So that was item no. 113 which relates to a hair. Item no. 115, I think that is one of the rear gate bloodstains. Item no. 116, a second rear gate bloodstain. I believe that is it. I think even on the glove and the sock there were still some traces I know in those general areas that we sampled. There was one area on the glove that we thought was tissue that that was consumed.
I'm sorry. In addition to--these are actually the swatch items or the initial evidence items. In addition to those items, was there--is there also extracted DNA left over from many of these items?
Well, yes. Most of those items there are--there is extracted DNA and for example, when I mentioned 115 and 116, those are those rear gate samples, there is extracted DNA from those left over. I think we mentioned the hair--the hair we haven't talked about earlier, but that work was done by Stephen Meyers in our laboratory and he did not detect any DNA in that extract, so that extract still remains. We didn't do my typing of that sample.
Okay. And as an example of what one can do with extracted DNA, is that what you sent to cellmark for their analyses on 13a1, the cutting from the sock?
So is it possible to--to do additional testing with that extracted DNA if one were to try to confirm results?
And in addition to extracted DNA, is there also something--the jury has heard from Dr. Cotton on these processes--amplified DNA that is as a result of the PCR process after DNA is amplified?
Yes. On most--almost all of these samples, in fact, there should be amplified DNA left over that is now residing in our PCR product room.
And as a forensic scientist do you feel that the best check on your analytical reliability is reanalysis of the evidence?
Sure. What could be done with you--as a forensic scientist you have got considerable experience before you worked for DOJ. What could one do with remaining swatch, let's say, from the same item.
What could one do with a remaining swatch, some extracted DNA and some amplified DNA?
Let's work backward. With the amplified DNA one has the PCR product already to go, so one could actually test that. To me that is probably not the most useful. Then the next approach would be to look at the extracted DNA and one could take that DNA and either run it through the same types of tests that we ran in our laboratory or run it in an additional genetic marker DNA test to gain more genetic information about a particular sample. Then one takes a further step back to the actual raw sample, the raw swatch itself, and certainly one can do one's own extraction and work on that material.
And is that just your opinion or have you relied on the opinions of others in the forensic science field?
Sustained. Let's move on in this area. You have established that it is available for other corroboration.
KEY QUOTEAll right. Mr. Sims, we have covered how you sample and evaluated some but not all of the items. I would like you to explain your problem solving approach. Your lab provides both RFLP and PCR services; is that true?
And for example, when this case was submitted to you with the first batch of stains, what was your initial plan to--what sort of test did you want to perform on those stains?
Well, initially we thought this might be an RFLP case all the way and our initial involvement in this case was very limited. If you would like I can go into a little bit of that history.
Yes. Initially we were planning to look at a very few number of samples to do RFLP testing in this particular case. As it turned out, some of those initial samples turned out to be in a degraded state and not suitable for RFLP analysis and in particular that would be the Bundy drops that--that we looked at in that initial series.
So is it fair to say that RFLP would have been the preferred approach if there was enough DNA and it was intact?
Yes, I think so, because the RFLP test is more discriminating. You have a much better chance of excluding somebody who is not really the source of those samples.
And at what point do--do these samples actually flow through the same possess in the beginning and then branch out, depending on how much DNA and how intact it is?
Yes. What we do is we do the initial extraction of the sample and then we evaluate to see whether or not we should proceed with the RFLP or the PCR approach.
Yes. In our laboratory we do. The type of extraction we do is designed so that we can use that DNA either for PCR or for RFLP, which is different than some laboratory's approach.
I don't have a real clear idea on what they are doing. They may do chelex type extractions. I think LAPD does chelex extractions also.
Okay. Do you have written protocols in your laboratory for performing RFLP in your lab?
There are variations on the theme. I mean, it is basically the same--the same process but different laboratories use, for example, different restriction enzymes. That is the enzyme that shoots in at a specific site. And also different laboratories use different probes to look at different sites of genetic variation in the DNA.
Okay. If you will, can we just compare the system that you have with the system in place at the FBI. Are you familiar with that?
Well, briefly, they have used the same restriction enzyme and data can be interchanged between the two and we have already had a reference to that much earlier on on compatibility of databases. That is one of the articles that Mr. Sims talked about of his qualifications.
I have no objection to him saying that they used the same restriction enzyme. I have a lot of problem if he is going to be qualified an as a population geneticist to talk about the appropriateness of using different databases. I don't think he is qualified to do that.
Very briefly, Mr. Sims, what is the compatibility or the similarity of the system in place at DOJ lab versus the FBI and many other labs in this country?
The main point is that we use the same restriction enzyme which is called hae-3, h-a-e-3, and also that we use the same probes, there is a battery of probes that overlap, and we have exchanged samples with the FBI to show that our data is compatible with their data.
Okay. And if you would, would you contrast the system that you use and the FBI and many other labs with Cellmark's because the jury has heard quite a bit of Cellmark's approach to RFLP.
Yes. The main difference is that they are using a different restriction enzyme for their analysis and I believe it is hin-f1 is their restriction enzyme and what it basically does is it gives larger DNA restriction fragments, so their stuff tends to band higher up on these gels that we look at. And I believe two of the probes that we use are the same probes as ours and I think there are three different ones that they also use, but it is the same fundamental process.
Now, cellmark has described--Robin Cotton described a cocktail probe which is a mixture of their single locus probes. Do you or the FBI use that same sort of cocktail?
Okay. Do you have controls built into your RFLP testing to measure how well the test has been performed in any given test?
Could you briefly describe the types of controls, specifically in the RFLP process, that you have and what their function is.
Yes. There are two main controls that we run on the RFLP on any particular autorad that you see. One will be what is called a k562 standard. That is a--a DNA--cell-cultured DNA that is run almost--not in every lab in the nation, but a lot of laboratories in the nation use that as a standard control. We know where the value should be for the two bands or sometimes one band that is produced by that particular standard. And so that provides us important information. It tells us that the probing was working correctly. And the sizing information is also checked that way. The second control that I--and I mentioned this a little bit earlier--was that we always run on an RFLP gel. We always run one of these quality control samples. That is a sample that is unknown to the analyst, and then the analyst goes through and determines what the band sizes are for that particular sample and then submits that data for review, so that is blind to the analyst.
Okay. That is--I think you mentioned the supervisor actually looks at what the true values are?
If there is a discrepancy between the two, we have never had one that I know of where we have mixed up anything. We have--I know in my case I had one particular sample where one band, a very high band, was slightly off because of a gel problem and then we rejected that entire data and I reran the entire experiment.
Okay. If you would, let's talk about how your PCR process works as opposed to the RFLP process. Just give us a little overview. What sort of markers do you use for PCR and DOJ lab?
Yes. The markers that we use for PCR, first off, would be the DQ-Alpha marker and that is the one that has been in most--perhaps the most widespread use in forensic science. It has got a fairly long history now of usage. Then the other--
The first case that I am aware of that that was used in was--it was Dr. Blake who pioneered the use of PCR in forensic science and that would be in 1986, I believe it is People versus Pestinikis, I think it is a Pennsylvania case. I may be wrong on the state.
And Robin Cotton described the type of process that that entails. Do you have an additional PCR marker?
Can you just briefly compare, contrast the method of testing of DQ-Alpha with D1S80?
Yes. The DQ-Alpha involves looking at a particular genetic locus that has variation in the DNA sequence and we can detect that in this typing procedure that we use, so we are actually looking at a little bit of variation in the sequence to detect that polymorphism or different form. On the other hand, the D1S80 is what is called a length polymorphism. It is somewhat like the RFLP procedure in that the different people have different lengths of this repeated sequence of DNA, but it is detected in a completely different manner than the DQ-Alpha is.
The jury has heard a great deal of testimony about substrate controls which we will discuss in a little while. Do you normally process substrate controls through the RFLP process?
No. Unless one saw that there was a substantial amount of DNA on the substrate control that could be succeeded to RFLP, one would not. They are really for the PCR.
Yes. The--the importance to me of the substrate controls is that that provides not only a way of evaluating the substrate, that the stain is on, whether it be a sidewalk or whether it be a garment or that sort of thing, but it also provides a way of evaluating how a sample is treated through the entire extraction and testing process. I mean, beginning with the scene, taking it all the way through the initial laboratory examination and then following it up with the--with the actual testing and typing procedure. And with PCR one is always on guard for contamination and that is one way of testing to see whether or not there is some contamination.
KEY QUOTEOkay. We will discuss that in a bit. So the substrate controls, if you have them in a given case, are processed through the PCR process from start to finish?
Can you give us any idea of how frequently you do not see substrate controls in cases?
We generally get them--we generally ask for them from our submitting laboratories, for example, the Bureau of Forensic Services field laboratories will submit substrate controls to us, but at times in my experience with certain types of evidence, one cannot always get a substrate control.
Are there a variety of what is to extract DNA? I think you mentioned the chelex extraction process?
Yes. There are a variety of ways to do it. Some of them are just modifications of a theme, but there are different approaches and people have looked at different ways of doing it.
We use what's called an organic extraction. We actually place the sample into a buffer that contains a soap solution and also an enzyme that chews up protein and that combination loosens up the DNA and gives you what hopefully will be free DNA, because you have to remember that DNA in the cell has protein wrapped around it, and so you have to free the DNA so that you can work with it and that is what the extraction process it.
Okay. Do you have a separate written protocol that describes the PCR process, the DQ-Alpha from start to finish?
Yes. We look at the protocols that are in existence in the scientific literature and we make some slight modifications of those.
Do the manufacturers of these products provide something in addition or something called a user guide?
Yes. They provide a user guide that explains some of the parameters of the kits and how they are used.
Perfect. All right. Ladies and gentlemen, we are going to take a 15-Minute recess. Please remember all my admonitions to you and we'll resume in fifteen minutes. And Mr. Sims, you can step down.
RFLP would have been the preferred approach if there was enough DNA and it was intact... the RFLP test is more discriminating. You have a much better chance of excluding somebody who is not really the source of those samples.
With the amplified DNA one has the PCR product already to go... Then the next approach would be to look at the extracted DNA and one could take that DNA and either run it through the same types of tests that we ran in our laboratory or run it in an additional genetic marker DNA test to gain more genetic information.
The importance to me of the substrate controls is that that provides not only a way of evaluating the substrate... but it also provides a way of evaluating how a sample is treated through the entire extraction and testing process... with PCR one is always on guard for contamination and that is one way of testing to see whether or not there is some contamination.
Let's move on in this area. You have established that it is available for other corroboration.