Before the break, Dr. Cotton, you had explained the PCR system of testing DNA. Is that a system that Cellmark uses in it's laboratory?

Yes.

Is that system used in laboratories, other than forensic laboratories, as well?

The reaction, the PCR reaction is used almost anywhere anybody's doing biology these days.

The specific test is used mainly in forensic laboratories and may have some application to other laboratories that are not doing forensic.

But the PCR process itself, that's very commonly used by DNA scientists?

PCR process itself is very common.

And in your laboratory, you use both RFLP test and the PCR test, as I understand it?

That's right.

Why do you choose one or the other?

Essentially it allows you to work on a lot of different kinds of evidence. Because if you have a lot of DNA and the DNA is in good condition, you can do an RFLP test and that gives you the most amount possible. The most possible information that you can get. If you don't have very much DNA, or it's not in very good condition, then you would go to a PCR test and you can still get some information from that test.

So are there different amounts of information that you can get from these different kind of tests?

Yes.

Could you sort of explain to us what the range of the amounts of information are that are available to you using these tests?

Yes. Let's -- in order to do that, and this is an -- this is an important concept, let me go back to the example I gave you where there's two alleles, an A and a B. And anyone, any person will be one of three types, an AA, a BB or an -- AA, an AB or a BB.

That system by itself isn't, doesn't have a lot of information because it's not going to be too unusual that two different people would both be an AA. So that system, by itself, allows you to exclude somebody if you have a piece of evidence that an AB, and you have a known individual that's an AA. The known can't be the contributor -- to the piece of evidence. But if you have a piece of evidence that's an AA and a known person that's an AA, that's going to happen fairly often just by chance; not necessarily because the person was the person who put the biological specimen on the piece of evidence.

The polymarker test altogether uses five systems like that. And so it provides a fair amount of information, particularly if you say, well, if I have two alleles, I can have three possible combinations.

And then I showed you, if you have three alleles, you can have six possible combinations. So that would be even a little more information.

But you could still accidentally, by chance have the same type as a piece of evidence.

For the DQ Alpha you have six alleles, 21 possible combinations, that's a little bit more information. So the chances of a person, person A accidentally having the same type as the DNA from a piece of evidence isn't so great.

RFLP, on the other hand, for each genetic location that you use, has at least 20 alleles. And for technical reasons that we haven't tried to explain, there may be actually many more than that.

So information that comes from an RFLP test is very highly discriminating and four genetic locations on an RFLP test or five or more, provide enormous amounts of information and have a very great ability to distinguish one person from the next.

So right now, as the technology stands, the most information possible is obtained from an RFLP test.

If you can't do an RFLP test and you do a PCR test, you are not getting the same amount of information. But it's still -- it's interesting to me, but it's still useful. What I mean to say, in that it allows you to exclude someone as being a contributor and then it allows to you include one as being a possible contributor. And then you can put a frequency to that to say, well, how often might you see this combination of genetic types. And if that number is one in 20, then you would see that combination relatively often.

If that number is one in a million, you wouldn't see that number very often.

And using the PCR test as an example, if you are able to test at several different of these genetic markers that you've talked about, does that increase the information that the test gives you?

It does. And that's really a good generic statement. The more genetic --

I'm going to object to the narrative response.

Overruled.

The more genetic locations that you look at, the more information you have.

(BY MR. LAMBERT) Now, before we get into the actual work that you did in this case, I'd like to ask you about some -- a word that we've heard used in this trial so far, and that has to do with degradation. What does degradation mean in the context of DNA?

In the context of DNA, it means that the DNA molecule is being broken down. Let's say that the DNA molecule is equivalent to a very long piece of thread. If I took a spool and unwound it, that would be one DNA molecule from one chromosome.

If I took a pair of scissors then -- and cut that thread in 20 different places. That might be the -- equivalent to that DNA being slightly degraded, that is it is randomly broken in 20 different locations. It's no longer all in one piece.

If you think of degradation, you can think of degradation as a one continuum; from no degradation to DNA being completely in tact, to extensive degradation, where all you have are AT pairs and AT pairs and CG pairs; and anything in between.

So if I took that same thread and I cut it into a thousand, cut it at a thousand spots, it's going to be in a lot smaller pieces and that would be more degraded than if I cut it in 20 places.

In doing forensic DNA work, is degradation something that you see very often?

It's something that you see all the time.

Why is that, Dr. Cotton?

If you take some fresh blood from -- if I had somebody draw my blood and we extracted the DNA from it right then, we would get DNA that's in very good condition, and might have been broken up a little bit just in the process of handling it, but it would be it would be really in good shape.

If you have blood or any other human cells left at a crime scene, that those cells are not in the body any longer and they are now subjected to whatever environment is at that crime scene, it might be sunlight. It might be heat. It might be -- there are a lot of different kinds of evidence.

It might be that some evidence is taken from someone who is deceased. So all of the things that are affecting those cells will eventually affect the DNA and it will gradually degrade. And depending on where it is and what conditions it's under, it may degrade more, or it may degrade less.

And are you, as a general proposition, able to test this degraded DNA to determine the information that you've described in the RFLP and PCR test?

Yes.

Does there ever come a point in time when the DNA is so degraded that you can no longer test it?

Yes.

And when that happens, Dr. Cotton, does the degradation change the DNA type from one type into another type?

No, it --

I'm sorry. Please.

It's okay. If it's too degraded to test, you simply don't get an answer.

And does DNA type ever change from one type into another type?

If --

Through degradation?

No.

And can degradation change DNA so that one person's DNA type could be mistaken for another person's DNA type?

The answer to that is no. I can think of an affect where you might lose some information by degradation, but it won't -- it won't change somebody's type to be something other than what it started to be. So you're -- you either have all the information that's there, you can lose some of it or you will lose all of it.

Okay. Now, let's talk about this test. Did you, at Cellmark -- did Cellmark receive evidence items to be tested in this case?

Yes.

Do you recall when you first received those?

I need to --

Take a look at your -- look at your records?

-- Yeah, use the case records.

The initial items that we received were received on June 24, 1994.

And who did you receive those initial items from?

From Colin Yamauchi.

And from whom is he employed?

LAPD Scientific Investigation Division.

And during the course of your involvement with this case, did you receive subsequent items of evidence from the Scientific Investigation Division?

Yes.

Did you receive from them, any other source?

Yes. We received, also, some tubes that had DNA already extracted. So the tubes contained DNA and the original extractions had been done at the California Department of Justice Lab in Berkeley.

And is that another DNA laboratory?

Yes, it is.

On this -- the initial time, when you got these evidence items that Mr. Yamauchi sent you, when you first processed those items, was anyone at your laboratory other than Cellmark people?

Well, when we first opened the items and logged -- Well, actually for the very first two items, no, there wasn't.

And how about the for the rest of the items?

For some of the subsequent items, we had Henry Lee and Edward Blake, Dr. Blake and Dr. Lee present in the lab to watch the items initially be put into tubes from which they would be processed.

And Dr. Lee and Dr. Blake were there as representatives of Mr. Simpson?

That's correct.

And Dr. Blake, is he, himself, a DNA scientist?

Yes, he is.

Does he run a laboratory that does DNA testing?

Objection. Irrelevant.

Overruled.

Yes, he does.

(BY MR. LAMBERT) Ultimately, do you have a record as to how many different evidence items were tested by Cellmark laboratories in this case?

Yes.

Can you tell me how many there were?

All together, we tested 23 items.

And were all those items tested by the one test or the other or did you use both of the tests described?

Some items were tested, both RFLP and PCR. And some items were just tested with PCR.

Why don't we bring out the next board, please.

This is 291, Your Honor.

(BY MR. LAMBERT) Before we get to this board, Dr. Cotton, I'd like to ask you a question about frequencies. You mentioned before there was a way to determine the frequency of some particular DNA type. Could you explain that to us please?

Yes. What you're doing is saying I have a group of genetic characteristics and I want to know how often they occur in the population. And traditionally, that question has been asked separately for different racial or ethnic groups.

So you might say, how often does this group of characteristics occur in Caucasians, how often does it occur in African persons, how often does it occur in Hispanics or Asians or whatever group you were interested in.

The purpose of doing that is just what I mentioned earlier. That is, if a genetic characteristics or a group of characteristics is common, that doesn't tell you a lot. You can exclude somebody if they don't share the characteristics of a piece of evidence. But if you include them, and that -- and half the population has that characteristics, it doesn't tell you very much.

On the other hand, if you calculate a frequency and say I have -- I have a set of genetic characteristics here and I'm going to ask the question, how often do they individually, each individually occur? And then if I want to say how often would they occur as a group, I can multiply how often each one occurs individually together. And that will tell me how often they occur as a group.

And if that frequency is rare, then that tells you a lot more about whether that individual, how likely it is that that individual was a contributor, as opposed to accidentally having the same type by chance.

And as part of Cellmark's regular work, do you routinely calculate these frequencies?

Yes, we do.

Do you include them in your reports, on your test result?

Yes, we do.

Did you do so in this case?

Yes, we did.

So for each of the items that you tested were you -- where you got a reportable result, you included a frequency calculation?

Yes, we did.

That's a calculation that is routinely done by other DNA laboratories; isn't it -- as well; isn't it, Doctor?

Yes.

Now let's take a look at this board itself. I'd like to focus your attention first, on item 56, which is a shoe print item. Did you do a test on that item?

Yes, we did.

And what test did you do?

We did a DQ Alpha and a polymarker test.

And those are the PCR tests that you mentioned?

They are both PCR tests.

And what results did you get on -- on that test?

The DQ Alpha result showed us a type of a 1.1 but the control that is included on this test, that basically is sort of a way to say I have enough DNA to confidently call this result, did not show-up.

So the -- if you look on the board in parentheses it says "zero." That's supposed to be -- anyway there's no C dot. That means there's no control dot. So we did not regard that as an interpretable result and the DQ Alpha result was then inconclusive.

We did get a polymarker match, that is the polymarker type from that piece of evidence was the same as Nicole Brown's polymarker type.

And looking up at the top of the board where we have the names Orenthal Simpson, Nicole Brown and Ronald Goldman and opposite each one of these those, would you describe what those letters mean at the top for the DQ Alpha entry?

Yes. The DQ Alpha entry shows what the type was from these three known individuals.

Mr. Simpson has a 1.1, 1.2 DQ Alpha type; Nicole Brown has a 1.1, 1.1 DQ Alpha type; and Ronald Goldman has a 1.3, 4, DQ Alpha type.

Than, though we don't have it on the board, did you also determine the five polymarker types for each of those three persons?

We did.

And as to number 56, you obtained a polymarker match at all five of those types for Nicole Brown?

Yes, we did.

So that would tell you then that Nicole Brown is a possible source of that item 56; is that right?

Yes, it would.

And were you able to exclude Mr. Simpson and Mr. Goldman as possible sources?

Yes. They are excluded.

So the only possible source upon those three people is Nicole Brown?

Among those three people, she's the only one that's not excluded.

And were you able to calculate a frequency for that one item?

Yes, we were.

Can you please write that frequency on the board for us in the space provided there?

We can't see behind here. Can you move it toward the judge, or just move it over?

Yeah. Thank you.

All the jurors see it?

Okay. Go ahead.

(BY MR. LAMBERT) Maybe black is better.

So for this one evidence item, you were able to determine the frequency as 1 in 48 to 1 in 110. Perhaps you could explain what those numbers mean to us?

For each item, we calculated a frequency for Caucasians, for African persons and for Hispanics, and they give different numbers.

What I wrote on the board was the smallest of those numbers, was 1 in 48. And the largest of those, the largest of those numbers was 1 in 110.

And taking the one in four, what does that number tell us, 1 in 48?

That means that we are estimating. And every time you do this, this is an estimate. Using a different reference sample, another estimate might be slightly different. It means that the combination of polymarker types that were common to those, from the shoe print and Nicole Brown occurs in about 1 in 48, whatever racial group that was. I'd have to look at the report. As a low range, just to give you a range or as -- as little as 1 in 110.

Okay. And in this instance you're frequency was calculated just based on the polymarker test?

Yes. Because the DQ Alpha test did not have a C dot. That was one clue. So we didn't include that in the frequency calculation.

Okay. Let's now go up to the top of the chart item 47, which is the first of the drops by the Bundy trail. And could you tell me what your first -- what test you ran on that particular item?

We ran, again, the DQ Alpha test and the polymarker test.

And what results did you get?

We got a DQ Alpha type 1.1, 1.2 and a polymarker type that was the same as Mr. Simpson's.

And the DQ Alpha type 1.1, 1.2 is that the same as Mr. Simpson?

It's also the same as Mr. Simpson's.

Would Mr. Simpson be a possible source of that particular evidence item?

Yes.

And would either of Nicole Brown Simpson or Ronald Goldman be a possible source of that item?

No. They are both excluded.

Okay. So once again, the only possible source among those three people for that evidence item is Mr. Simpson; is that correct?

For that item of these three people we have the only one that could be a contributor.

Did you do a frequency allocation for that evidence item?

Yes, we did.

Can you please put that up on the board for us?

So in regard to that particular evidence item, you would expect to find that combination of DQ Alpha types and polymarker types in about 1 out of every 5200 to about 1 in every 56,000 people?

Yes.

Is that what that means? The reason why that number is so much larger than on item 56 is what, Dr. Cotton?

In this case, we're now including and multiplying together, the DQ Alpha information and the polymarker information. So we have five locations that we looked at on the shoe print, five pieces of information here on the -- item 47, there are six pieces of information and it does result in a larger range of numbers.

But also, we're looking at a different set of types, too so, you can't make a direct comparison there.

But is that, at least, in part, an example of the more genetic markers that you are able to type, the high your frequency numbers can become?

Yes. But that you -- yeah. But if you really wanted to make that comparison, you'd take the type from the shoe print and then add a DQ Alpha information to that, then you'd see a better relative number.

Okay. Let's take now, item 48. Again, what tests were you able to do on item 48?

We did the DQ Alpha test and the polymarker test.

And the results on that test?

The results on that test for DQ Alpha are type 1.1, 1.2. The polymarker types are the same as the types obtained from Mr. Simpson. Nicole Brown and Ronald Goldman are excluded: As possible contributors.

And when you say excluded in this context does that mean that they could not possibly be the source of that blood evidence?

Yes.

And Mr. Simpson could be the source; is that what your saying?

Yes.

And I probably know the answer to this by looking at the board, but can you tell me what the frequency calculation for that particular evidence item was?

It's exactly the same as the one for item 47 because it's exactly the same set of types.

Okay. And now how about item number 49?

Item 49, we did a DQ Alpha test and a polymarker test. The DQ Alpha has a 1.1, 1.2 type polymarker, the set of polymarker types are the same as the types obtained from Mr. Simpson's known sample.

So once again, Mr. Simpson is a possible source for this item of evidence?

That's right.

And Ronald Goldman and Nicole Brown Simpson are excluded?

That's correct.

Would the frequency for that evidence item be the same?

Yes, it would.

Let's now then go to item 50. And by the way, I'm just asking you about the Cellmark tests here. Other labs tested some of these same evidence items?

That's right.

So Cellmark's tests on item 50 showed -- first, was the PCR and RFLP test?

It's a PCR test.

What's the results there?

The results are that the DQ Alpha type is 1.1; 1.2. The polymarker set of -- typed of the same as those for Mr. Simpson he is a possible source. He's not excluded. Nicole Brown and Ronald Goldman are excluded.

Get down or take down our patch for this one..

Once again, from the frequencies for that item be the same as for item 47?

Yes, it would.

That's because those are the same types.

That's right.

Why don't we have you write those up there now, so we'll have our record complete. I hope you can reach that top line.

Now as to item number 52, possibly should have you do this before you sat down. As to item number 52, did you also do a PCR test on that item, which is the last of the five drops along the Bundy walkway?

Yes, we did.

And what results did you get there?

We got a DQ Alpha type 1.1, 1.2. We got a polymarker set of types that's the same as Mr. Simpson's.

And would he, once again, therefore, by the CPCR test be included as a possible source of that evidence item?

Yes.

And would Ronald Goldman and Nicole Brown Simpson be excluded?

Yes, they would.

Now, as to that evidence item, were you also able to do an RFLP test?

Yes, we were.

The reason why you could do it on that evidence item and not the other evidence items is what?

And the RFLP test that you did, what results did you obtain?

We looked at five different genetic locations with the RFLP test and the DNA banding pattern that we obtained from those five locations matches, the DNA banding pattern for Mr. Simpson.

By banding pattern, you mean by what you showed us on that example before Mr. Simpson's bands appearing on the Autorad at those five genetic locations, matched the bands that the sample created. Is that --

That's right.

So is Mr. Simpson therefore under both the PCR test an the RFLP test included as a possible source of this evidence item?

Yes.

And is Ronald Goldman and Nicole Brown Simpson excluded?

They are excluded.

Now, because you have two different tests here, did you do two different frequency calculations for that evidence item?

We did one frequency calculation for the DQ Alpha polymarker and we did a -- we did a separate calculation for the RFLP results.

And would the frequency calculation for the PCR results be the same as for the other four evidence items?

Yes, it is.

And that's because ...

That's because it's the same set of types that we're doing the calculation for.

The frequency calculations for the five -- by the way, let me ask you this first: When we say on our chart here, five probe match, can you explain what a probe is?

A probe is recognizing a specific genetic location so when they, on the chart where it says five probe match, that means five RFLP genetic locations we looked at.

And taking into account that five probe match, were you able to calculate the frequency, for the RFLP test, match that blood drop to Mr. Simpson's type?

Yes.

Could you put that calculation up for us, please?

And do you want the PCR calculation?

Might as well put it while you're at it.

(Witness complies, marks exhibits under frequency column for item numbers 52 52 and 56.

So, Dr. Cotton, you put up, for the PCR test results, the same numbers, the same frequency numbers that you found for the other blood drops along the Bundy trail, but obviously the frequency numbers that you found, using the RFLP test, are significantly higher. Could you please explain why that is to us?

It's because the RFLP test is very much more powerful in discriminating one person from the next. Any particular RFLP banding pattern is not a common event.

This particular pattern calculates out to be -- Occur in this range of 1 in 170 million people to 1 in 1.2 billion people. What it means, it's not a common occurrence so the likelihood that someone would, by chance, have this banding pattern is small.

As small as 1 in 170 million people?

Yes.

Okay. Now, we haven't put all of the test results that you got in connection with the Bundy crime scene on this board. But I'd like to ask you about one other one that you did.

Did you do some testing on evidence item number 84?

Yes.

Can you tell us what evidence item number 84 is, please.

The --

The item was broken down into -- there's fingernail clippings, fingernail scrapings from the right and left hand.

And those are from the Nicole Brown fingernail scrapings?

That's right.

From whom did you receive those fingernail scrapings?

We received extracted DNA from the California Department of Justice Lab.

And did you subject those fingernail scrapings to any tests?

Yes, we did, the PM and the DQ Alpha test.

What test results did you get?

The test results we got were the same types as Nicole Brown's types.

So the DQ Alpha type for the blood from under the fingernails was 1.1, 1.1?

That's right.

The polymarker types in this AB, B system that you described before that matched Nicole at all five of those polymorphic marker locations?

That's right.

These tests, this PCR test that you did on the fingernails, that's a sensitive test; isn't it?

Yes.

And did you -- would you be able to determine from that test if any other person's blood was in with the blood that you tested?

In other words, if there was more than one person's blood in there?

Well, I have to answer that yes and no.

Okay.

Yes. It's a sensitive test, but it does have limitations. So you have to have enough blood to get a result. You could have a mixture of two people and have so little of one person and so much of the second person, that you would only see the major contributor.

You could have a mixture of two people where the amounts in that mixture were more -- were more even and you would see both people.

So, yes, it's a sensitive test. It will not always pick up a mixture, but it can pick up a mixture if two components are there in amounts. At least that would reflect a 1 to 20 or a -- or above. That is, the parts would be present 1 to 20 or one to one in that range.

In other words, if you had one part of one person's blood and 20 parts of another person's blood, you could detect both of their blood types?

You would possibly see that you had a mixture if you had one part, one part of one and five parts of the other, you would do that even better. If you had one part of one person and a hundred parts of another person, you wouldn't see that.

And in this particular test for evidence item 84, did you see any evidence of any additional person other than the one who's types you obtained?

No.

Why don't we have the next board then.

This will be -- excuse me, I believe 296.

(BY MR. LAMBERT) Now, Dr. Cotton, this board reflects some additional evidence items. These from Mr. Simpson's Rockingham residence.

Did Cellmark test some of those items?

Yes, we did.

And first let's take item number 7 with a -- was a blood drop found on the driveway there? Were you able to do a test on that item?

Yes, we were.

And what were your results?

We have again visible, DQ Alpha results have a 1.1, 1.2. But like one of the samples on the previous board, there was no C dot there, so the DQ Alpha results on this particular test were inconclusive and were not used in determining the frequency.

The polymarker results were the same as those obtained from Mr. Simpson.

And would that test therefore include Mr. Simpson as a possible source of that evidence item?

Yes.

And did it exclude Nicole Brown or/and Ronald Goldman as possible sources?

Yes.

So we can take a little patch off on this one. And did you calculate a frequency for that particular type?

Yes, we did.

Could you please put that on the board?

There's a second item on this Rockingham evidence board which is item number 12, collected in the foyer of the house at Rockingham. Were you able to do tests on that evidence item?

Yes, we were.

And what tests were you able to perform on that evidence item?

We did a DQ Alpha and a polymarker test and also an RFLP test.

And so you were able to do much more testing on this evidence item than on evidence item number 7?

That's right.

And do you have any idea as to why one item would test so much better than the other item?

It's a matter of how degraded the DNA was. The DNA from the foyer was in good condition. The DNA from the driveway was not.

So the location at which an evidence item is found can affect how degraded the item would be.

Objection. Leading.

Overruled.

Definitely.

(BY MR. LAMBERT) Now, did you do calculations for both the DQ Alpha and RFLP for the evidence item?

Yes, I did.

I guess before we did that, I should take off this patch because this also includes Mr. Simpson as a possible source, didn't it?

It does.

And neither Ronald Goldman or Nicole Brown Simpson could be included, could they?

That's correct.

Would you put the frequencies in, please?

Yes.

And the number that you have placed up here is for both the PCR and RFLP. Those are the same numbers that we saw on the Bundy results board?

That's right.

That's because you got the same test results there?

Yes.

And once again, for that RFLP test of the blood drop found in the foyer, only somewhere between 1 and 170 million and 1 and 1.2 billion people would have those -- that five probe type?

That's the estimate.

Why don't you take that down? (Mr. Foster complies.)

Can I have the next one?

(BY MR. LAMBERT) The next board is 297. Entitled "Results of DNA Analysis Rockingham Socks."

Before we get to this board, Dr. Cotton, let me ask you, did you also do any testing on any of the substrate controls for these evidence items?

Yes, we did four substrate controls.

And could you explain to us again briefly what a substrate control is?

All right. Thank you. Somebody else might have.

Somebody else might have.

Essentially, if you have a stain, you would be taking an area of the cloth that is not obviously stained, but adjacent to the stained area. Or if you were lifting a stain from a surface, you would lift your stain up and then you would take another lift from an area adjacent to the stain that was not apparently stained.

And for evidence item 7, which was the blood drop in the driveway at Rockingham that we just looked at, did you test the substrate control for that evidence item?

Yes, we did.

And what result did you get?

We got no detectable result.

So that you could not find any detectable DNA in that substrate?

That's right.

And for evidence item number 12, which was blood drop at the foyer that you got the RFLP result on. Did you test the control for that evidence item?

Yes.

What result did you get?

No detectable DNA.

And for evidence item 49, which is one of the blood drops at Bundy we looked at earlier, did you test the control for that item?

Yes, we did.

And what result did you get?

No detectable DNA.

And for evidence item 56, which was the bloody shoe print at Bundy that we looked at earlier, did you test the control for that item?

Yes, we did.

And what result did you get?

No detectable DNA.

Thank you.

Now, let's take a look at this board, and this deals with a pair of socks found at Rockingham. Did you do any tests in regard to that particular evidence item?

Yes, we did.

And what kind of test did you do?

We did a PMDQ Alpha test and an RFLP test.