[00:00:02] Speaker 01:
Our third case this morning is number 181587 Pacific Bioshares of California versus IPC.

[00:00:54] Speaker 01:
Okay, Mr. Rinus.

[00:00:58] Speaker 04:
Thank you, Your Honor.

[00:00:59] Speaker 04:
Edward Rinus on behalf of PacBio.

[00:01:02] Speaker 04:
The ITC improperly included a synthesis step.

[00:01:06] Speaker 04:
It actually added a synthesis step to the patents in suit by misconstruing the claim term single molecule sequencing.

[00:01:13] Speaker 04:
The main argument is that the patent describes the invention as single molecule sequencing with a synthesis step.

[00:01:24] Speaker 04:
That is not so.

[00:01:25] Speaker 04:
And the main reason why that's not so that I wanted to explain here today is the hairpin invention of the patent, which is the innovation that's the subject of the claims and that's being infringed, is independent of how you do the sequencing itself, whether you use a synthesis step or you just do single models.

[00:01:43] Speaker 01:
Well, how do we know that?

[00:01:44] Speaker 01:
I mean, the problem is, and I guess you don't dispute this, that the specification only describes

[00:01:54] Speaker 01:
template sequencing and not nanopore sequencing.

[00:01:57] Speaker 04:
No, there's a subtlety there.

[00:01:59] Speaker 04:
So the experimental results that are shown are with the commercial product of PacBio that includes a synthesis step.

[00:02:07] Speaker 04:
But there are definitely shown alternative approaches.

[00:02:10] Speaker 04:
There are, for example, magnetic particles, semiconductor crystals.

[00:02:14] Speaker 04:
Basically, the patent at column seven says you can use a variety of ways actually doing the sequencing.

[00:02:20] Speaker 04:
I think where the confusion comes in.

[00:02:21] Speaker 01:
Well, where does it say that?

[00:02:23] Speaker 04:
column seven at line 36 through 41.

[00:02:29] Speaker 04:
In preparing for argument, what I thought the concern was is this is an omnibus patent application that covers a whole variety of inventions.

[00:02:45] Speaker 04:
It's not a one invention

[00:02:47] Speaker 04:
This is a major innovation.

[00:02:50] Speaker 01:
Wait, wait, wait.

[00:02:51] Speaker 01:
In column seven, you're not contending that that includes nanopore sequencing, right?

[00:02:57] Speaker 04:
Well, I mean, down certainly at line 54, it specifies nanopore sequencing.

[00:03:02] Speaker 04:
And it refers to the Clark reference as an example.

[00:03:05] Speaker 00:
Well, no, it refers to nanopore sensors, not nanopore sequencing.

[00:03:10] Speaker 04:
That is the definition.

[00:03:11] Speaker 04:
If you have a nanopore sensor, then you're doing nanopore sequencing.

[00:03:14] Speaker 04:
There's no other.

[00:03:15] Speaker 04:
I mean, that's what it is.

[00:03:18] Speaker 03:
Well, the ITC found to the contrary.

[00:03:21] Speaker 03:
They ultimately concluded that reading this paragraph as a whole, what must be going on here is some version of synthesis.

[00:03:31] Speaker 03:
And then once you have your strands with your labels, you're then using the nanopore sensor.

[00:03:38] Speaker 03:
And then it's a little unclear in this spec whether you're using the sensor to identify the labels or an entire

[00:03:47] Speaker 03:
synthesized strand?

[00:03:49] Speaker 04:
Well, it references the Clark paper, which is a well-known paper in the field, so a person skilled in the art would know exactly what it is.

[00:03:54] Speaker 04:
It's undisputed by the ITC that what Clark shows is non-synthesis nanopore sequencing.

[00:04:02] Speaker 04:
That's in the ITC's brief at 36.

[00:04:06] Speaker 04:
So how much do you have to show?

[00:04:10] Speaker 04:
You actually have nanopore sequencing here, but the point that I want to raise is that

[00:04:14] Speaker 04:
This patent is an omnibus patent about a whole variety of different inventions.

[00:04:18] Speaker 04:
I'm sure there are inventions that involve synthesis.

[00:04:21] Speaker 04:
And the preferred embodiment was clearly the focus of the author.

[00:04:24] Speaker 04:
But what is critical here is to understand what the claimed invention is, which is the hairpin.

[00:04:31] Speaker 04:
And the brilliance of it is you have a single DNA where you take the double DNA strand, and then you separate it out.

[00:04:39] Speaker 04:
You have to put a linker in, and you sequence one after the other.

[00:04:43] Speaker 04:
That has nothing to do with how the particular sequencing is done.

[00:04:46] Speaker 04:
In fact, and this is where this case would be unprecedented in my view, is in the prosecution industry to demonstrate the unexpected benefits of the invention using the Harpon invention.

[00:04:58] Speaker 04:
It doesn't seem like there's even a debate about that.

[00:05:01] Speaker 04:
Again, the ITC decision itself says it's undisputed that Oxford uses the invention and gets great results with it.

[00:05:10] Speaker 04:
And that was what was cited in the declaration

[00:05:12] Speaker 04:
to show unexpected results.

[00:05:15] Speaker 04:
And so to say that the examiner looked at the publications of Oxford that definitely don't involve synthesis, that's in the record, and said, OK, this shows how great it works.

[00:05:30] Speaker 04:
And it's a non-synthesisist reaction.

[00:05:33] Speaker 04:
And then it's granted on the basis of that.

[00:05:36] Speaker 03:
What if I look through that prosecution history discussion and see that

[00:05:42] Speaker 03:
that based on the discussion between the applicant and the examiner, the focus is really on the construct of this strand, single strand with the hairpin, and it doesn't have anything to do.

[00:05:58] Speaker 03:
And so therefore, the allowance isn't triggered based on what kind of sequencing is being used there, whether it's nanopore or whether it's synthesis or something like that.

[00:06:09] Speaker 04:
This is the whole point of what I'm trying to argue.

[00:06:11] Speaker 04:
And that's the whole focus, which is that the examiner granted the patent by saying, this is great for single molecule sequencing.

[00:06:18] Speaker 04:
They were trying to claim it in their own patent.

[00:06:20] Speaker 04:
We have that in the record.

[00:06:20] Speaker 04:
They don't even deny it.

[00:06:21] Speaker 04:
They don't address it.

[00:06:22] Speaker 04:
It's good for single molecule sequencing, regardless of whether synthesis is possible.

[00:06:26] Speaker 03:
But I guess for our purposes here, the real question is, how do we understand single molecule sequencing as that term is used in the claims of this patent?

[00:06:34] Speaker 03:
And so when we look at this patent, I understand your point, which

[00:06:39] Speaker 03:
I think makes some sense, which is if we can say point of novelty, the point of novelty here isn't the specific kind of sequencing, whether it's by synthesis or by something else.

[00:06:48] Speaker 03:
OK, you get it.

[00:06:49] Speaker 03:
It's the idea of using this linker, this hairpin, to create this single strand out of the ordinary double strand.

[00:06:59] Speaker 03:
But the question is, that doesn't mean that we have a rule under the law that an inventor can't

[00:07:10] Speaker 03:
characterize something in the prior art in a new, different way for the inventor's own purposes.

[00:07:16] Speaker 03:
And so the real question is, how did this applicant, this inventor, use the term single molecule sequencing?

[00:07:26] Speaker 01:
It was 2008, 2009, right?

[00:07:28] Speaker 01:
Right.

[00:07:30] Speaker 04:
So it's really not subject to dispute that single molecule sequencing means sequencing a single molecule.

[00:07:36] Speaker 04:
So we're starting from the premise of adding in a limitation.

[00:07:40] Speaker 04:
Because in fact, that was what the prosecution history said is this only makes sense.

[00:07:45] Speaker 04:
This idea of using the hairpin only makes sense if you're doing one molecule at a time.

[00:07:50] Speaker 04:
If you're doing a group to just figure out what the group does, then keeping the integrity of the two pieces together doesn't have any value.

[00:07:58] Speaker 04:
That was what the declaration stated in the prosecution history.

[00:08:02] Speaker 04:
So everyone was focused single molecule sequencing versus non-single molecule sequencing.

[00:08:07] Speaker 04:
The examiner relied on unexpected benefits of something that the ITC held isn't within the scope of the claims.

[00:08:15] Speaker 04:
So a person reading the file history would clearly recognize it.

[00:08:19] Speaker 04:
But more importantly, the patent was granted with everyone knowing.

[00:08:22] Speaker 04:
There's the pending claims, which create a presumption that single molecule sequencing is a broader term.

[00:08:29] Speaker 01:
There's the- What do you mean, everybody recognizing?

[00:08:33] Speaker 01:
I mean, first of all,

[00:08:36] Speaker 01:
Your expert's declaration does not say what the understanding of single molecule sequencing terminology was back in 2008 and 2009, right?

[00:08:47] Speaker 04:
It's the admission of the other side's expert that the standard terminology in the RF.

[00:08:51] Speaker 01:
No, no, no, but stick with me.

[00:08:52] Speaker 01:
Okay.

[00:08:53] Speaker 04:
I'm with you.

[00:08:54] Speaker 01:
Okay?

[00:08:55] Speaker 01:
In the statements, in the declaration submitted in prosecution, your expert did not address

[00:09:02] Speaker 01:
the meaning of that terminology in 2008, 2009, correct?

[00:09:07] Speaker 04:
Disagree.

[00:09:07] Speaker 04:
He put in two references, Gupta and Postma, to show the meaning, and both were prior art references.

[00:09:13] Speaker 04:
So he specifically showed how the meaning in the art was.

[00:09:16] Speaker 04:
I totally disagree with that.

[00:09:18] Speaker 04:
The whole point of the declaration was to say nanopore sequencing was known as one of the species of single molecule sequencing.

[00:09:24] Speaker 04:
And Gupta and Postma are intrinsic evidence of what nanopore sequencing has at the time.

[00:09:30] Speaker 04:
And he said, this is what

[00:09:32] Speaker 04:
Single molecule sequencing covers it.

[00:09:34] Speaker 04:
It covers this, and then you cite.

[00:09:36] Speaker 01:
So you're getting from the citation of these references that it was the same in 2008, 2009.

[00:09:43] Speaker 01:
OK, but we have a series of cases, Biogen, there are others, which say that statements by the patentee trying to expand the scope of a claim during prosecution are not to be given any weight.

[00:09:57] Speaker 01:
How do you deal with that?

[00:09:59] Speaker 04:
I deal with it simply.

[00:10:00] Speaker 04:
The opposing expert, point blank, said the standard terminology in the art was that now... Okay, but that's it.

[00:10:07] Speaker 01:
You keep shifting to a different point.

[00:10:09] Speaker 01:
I'm talking just stick... Oh, okay.

[00:10:11] Speaker 01:
Yes, I'm not... Why under these cases should we give any weight to a statement expanding the scope of the claims during prosecution by the patentee when the cases say that we shouldn't do that?

[00:10:28] Speaker 04:
Let me be clear, because there's so much supporting evidence for the basic proposition that it's just further evidence that everyone's on notice.

[00:10:35] Speaker 01:
So you agree then we have to find support for your position outside of those statements in the prosecution history?

[00:10:43] Speaker 04:
I don't think any one piece of evidence here carries the day.

[00:10:46] Speaker 04:
And I definitely don't think that what the decision is based on

[00:10:51] Speaker 04:
So what are we adding in the face of all this evidence, the presumption against the interpretation, the fact that the patent was granted based on an embodiment that's outside of the construction, the definition in the file history under oath supported by prior art, the plain meaning single molecule sequencing doesn't have a synthesis step, the fact that the claim's long and has all kinds of other claim steps that are not sequencing,

[00:11:17] Speaker 04:
In view of all that, what is the real basis?

[00:11:19] Speaker 04:
The real basis is a sentence with the present invention that says, generally, broad, and particularly preferred embodiment and biometric.

[00:11:28] Speaker 03:
I think the I can see in the ALJ focused on more than just a single sentence.

[00:11:32] Speaker 03:
And if only there was a single sentence, then I understand your point.

[00:11:36] Speaker 03:
But the spec is quite pervasive and repetitive in its discussion of synthesis.

[00:11:44] Speaker 03:
And it seems to devote a lot of attention

[00:11:47] Speaker 03:
discussing a lot of different processes within the ambit of synthesis.

[00:11:53] Speaker 03:
And the summary of the invention repeatedly talks about synthesis.

[00:11:56] Speaker 03:
And so I guess one could arguably have a takeaway from reading the summary and then the opening columns of the detailed description that this inventor was

[00:12:08] Speaker 03:
entirely devoted to the idea of doing the sequencing through synthesis.

[00:12:12] Speaker 03:
And I think that's what was the hook for the ITC.

[00:12:15] Speaker 03:
And as we all know, the specification is the single best guide to understanding the claim.

[00:12:20] Speaker 03:
And so even if a particular claim term had an established meaning, it's an established technical meaning at the time of the invention to skilled artisans, there's nothing stopping an applicant from

[00:12:34] Speaker 03:
recharacterizing that established meaning to mean something specific for his own purposes in a patent.

[00:12:40] Speaker 03:
I think that's the focus of the debate here.

[00:12:43] Speaker 03:
And that's something we need to hear your answer on.

[00:12:46] Speaker 04:
My answer on that is the gestalt of the patent.

[00:12:49] Speaker 04:
This would be the high-order mark for this.

[00:12:51] Speaker 04:
Forget about all the other evidence I just recited.

[00:12:54] Speaker 04:
And it's the gestalt.

[00:12:55] Speaker 04:
What I'm saying is there's a lot of different inventions in here.

[00:12:58] Speaker 04:
So the repetition of synthesis could relate to a lot of things.

[00:13:02] Speaker 04:
What's important is that everyone agrees the invention is independent of synthesis step.

[00:13:06] Speaker 04:
And the patent does have the column seven discussion, which says, although described in terms of the specific smart sequencing process, the sequencing compositions of the invention, which include the hairpin, the nucleotide analogs may be detectable by any of a variety of different mechanisms.

[00:13:25] Speaker 03:
And then the sentence keeps going.

[00:13:26] Speaker 03:
There's no period there.

[00:13:28] Speaker 03:
It says, including the presence of fluorescent dye labels coupled to the nucleotide through a beta, et cetera, et cetera.

[00:13:34] Speaker 03:
And then the rest of it seems to be, again, turning us right back into the world of synthesis.

[00:13:42] Speaker 04:
There's no word synthesis there.

[00:13:44] Speaker 04:
I don't agree with that.

[00:13:46] Speaker 04:
And then it cites nanopore sensors and then cites an article

[00:13:52] Speaker 04:
That everyone agrees, not everyone agrees, the ITC agrees, discloses regular nanopore sequencing without synthesis.

[00:13:59] Speaker 04:
So he cited an example of nanopore sequencing, single molecule sequencing without synthesis.

[00:14:04] Speaker 04:
Like, how much do you, I mean, I've given about seven sources of evidence that tell you that this should be more.

[00:14:09] Speaker 06:
Is Dr. Erlich your expert, Ryan?

[00:14:12] Speaker 06:
Yes.

[00:14:14] Speaker 06:
Do you agree with his test, that his testimony was that in 2008, single molecule sequencing

[00:14:22] Speaker 06:
didn't have a well-established meaning, and it wasn't until maybe 2011.

[00:14:27] Speaker 04:
Absolutely not.

[00:14:28] Speaker 04:
And the fact that the ITC relied on that for that proposition tells me that that was result-oriented, I hate to say.

[00:14:36] Speaker 06:
Because if you look at it... Well, I went and looked at the testimony, and he says, mm, 2010, 11.

[00:14:42] Speaker 04:
He says that there was error rate.

[00:14:44] Speaker 04:
The question was whether that was known about error rates.

[00:14:47] Speaker 04:
The question had nothing to do with definition.

[00:14:49] Speaker 04:
And he said, the commercial systems weren't out there so that you wouldn't have an appreciation for the error rates at that point.

[00:14:57] Speaker 04:
And there's additional testimony where he makes that real explicit.

[00:14:59] Speaker 04:
But if you look at that, you'll see.

[00:15:00] Speaker 04:
I'd like to reserve my time.

[00:15:02] Speaker 06:
I do, but I'll do it when he comes back up.

[00:15:10] Speaker 06:
Did you have something more?

[00:15:11] Speaker 03:
Yeah.

[00:15:13] Speaker 03:
Would labels be used in nonsynthesis?

[00:15:18] Speaker 04:
There's so many ways you could use it.

[00:15:21] Speaker 04:
I would say not traditionally to just to be responsive.

[00:15:23] Speaker 04:
But I definitely wouldn't preclude the possibility that labels could be used in a system where you're cleaving the bases as they go through.

[00:15:33] Speaker 04:
I mean, I assume that you actually could probably do it that way.

[00:15:36] Speaker 04:
So I think looking at the actual literature that's cited, which shows what's consistent with the art, including the intrinsic prior art in the record, is a better way to determine what is intended by 904 cents.

[00:15:48] Speaker 06:
I'm going to read to you from 406, which is what I had looked at.

[00:15:54] Speaker 06:
That's 5983, depo page 406.

[00:16:03] Speaker 06:
I would say that before the person of general skill in the arts was actually really aware, you know, of single molecule sequencing and aware of that type of thing probably was another couple of years.

[00:16:17] Speaker 06:
It probably would have been like 2010 or something like that, maybe 2011.

[00:16:22] Speaker 04:
That type of thing being the error rate.

[00:16:27] Speaker 06:
You know of single molecule sequencing.

[00:16:30] Speaker 06:
That type of thing.

[00:16:31] Speaker 04:
I mean, we could all read it, but in view of all the literature, everything else, to rely on that to contest their own experts said the standard terminology and the art in 2008, 2009,

[00:16:45] Speaker 04:
was that single molecule sequencing encompassed nanopore.

[00:16:48] Speaker 04:
It's a single molecule.

[00:16:49] Speaker 04:
What else is there?

[00:16:51] Speaker 04:
I mean, it's not really debatable that single molecule sequencing encompasses nanopore.

[00:16:56] Speaker 01:
I guess if it weren't debatable, we wouldn't be here.

[00:16:58] Speaker 04:
No, it's the reliance on the, if you actually read the opinions, it's the reliant, the over reliance on the present invention sentence.

[00:17:05] Speaker 04:
It's not a serious statement.

[00:17:07] Speaker 04:
They just say that the extrinsic evidence is ambiguous.

[00:17:09] Speaker 04:
They don't

[00:17:10] Speaker 04:
They're not denying that nanopore sequencing means single molecule sequencing.

[00:17:14] Speaker 06:
I'll look at the prior language.

[00:17:15] Speaker 06:
I looked at that block in his testimony.

[00:17:19] Speaker 06:
I'll look at the prior language to see if it goes.

[00:17:22] Speaker 04:
Look around, and you see that it's referring to a commercial system.

[00:17:24] Speaker 04:
It's like the commercial systems are out.

[00:17:26] Speaker 04:
That's when people knew about the error rate.

[00:17:27] Speaker 04:
That's a total misuse.

[00:17:28] Speaker 04:
And that records an avalanche on the other side.

[00:17:31] Speaker 01:
All right.

[00:17:32] Speaker 01:
We'll give you two minutes for a bottle.

[00:17:36] Speaker 01:
Thank you, Your Honor.

[00:17:36] Speaker 01:
Ms.

[00:17:37] Speaker 01:
Naivella?

[00:17:43] Speaker 02:
May it please the court.

[00:17:45] Speaker 02:
I'd like to start where Judge Wallach ended at appendix page 5983 regarding the testimony of PACBIOS expert Dr. Ehrlich.

[00:17:56] Speaker 02:
The question was asked whether or not single molecule sequencing was error prone in 2008, which is the claim priority date for the independent claims at issue here.

[00:18:07] Speaker 02:
At page 405, Dr. Ehrlich at line 25 responds, yeah,

[00:18:13] Speaker 02:
He answers the question.

[00:18:15] Speaker 02:
Then he proceeds to add, although most people really didn't have an understanding of single molecules, unless you were on the leading edge, continuing on to page line five, most people didn't have much of a sense of a single molecule at all.

[00:18:29] Speaker 02:
Line eight, I would say that before the period, before the person of general skill in the arc was actually really aware, you know, of single molecule sequencing and aware of that type of thing, probably was another couple of years.

[00:18:43] Speaker 02:
So a couple of years after 2008, the time of the invention here, there was no well-established meaning of the term single molecule sequencing.

[00:18:53] Speaker 03:
What about the other side's expert that very, very clearly proclaimed that nanopore sequencing was a known, understood way of performing single molecule sequencing as of the time of the invention that's reinforced by the prior art references cited on the face of this patent, Gupta and Postma.

[00:19:12] Speaker 03:
I'm not saying anything wrong, am I?

[00:19:15] Speaker 03:
Well, Oxford's expert... Am I saying something wrong?

[00:19:18] Speaker 02:
Oxford... I wanted to clarify that statement.

[00:19:22] Speaker 02:
Oxford's expert testified as to the standard terminology of the term in the period of 2008 to 2009.

[00:19:28] Speaker 02:
Now, in 2008, single molecule sequencing and nanopore sequencing were nascent technologies.

[00:19:36] Speaker 02:
So we have these references to Gupta and Postma.

[00:19:39] Speaker 02:
Those were all published months after March 2008.

[00:19:43] Speaker 02:
And if you actually look at Gupta and Postma... So I'm trying to understand.

[00:19:48] Speaker 03:
The other side's expert acknowledged that single molecule sequencing encompassed nanopore sequencing as of the time of this invention.

[00:19:57] Speaker 03:
Is that fair?

[00:19:58] Speaker 03:
I understand you want to say it was nascent technology.

[00:20:01] Speaker 03:
That's fine.

[00:20:02] Speaker 03:
But nevertheless, he said what he said.

[00:20:05] Speaker 02:
I believe it's the 2008 to 2009, while it may cover the time of invention, it is not limited to the time of the invention, which is March 2008.

[00:20:15] Speaker 02:
So at the time of March 2008, nanomolecule sequencing and single molecule sequencing was not customary.

[00:20:26] Speaker 02:
It was not a customary term.

[00:20:27] Speaker 02:
And it was through the year, through the months, spanning into 2009, where there became a better understanding of the term.

[00:20:34] Speaker 03:
Is that what the experts said?

[00:20:36] Speaker 03:
I don't remember the expert saying it like that.

[00:20:38] Speaker 02:
If we look at appendix page 5, 4, 3, 2, at page 86 of Dr. Romsberg's deposition at lines 10 through 15,

[00:21:04] Speaker 02:
The question was, to a person of ordinary skill in the art, in the 2008 to 2009 time period, in terms of the standard terminology in the art, single molecule sequencing would encompass nanocore sequencing, correct?

[00:21:18] Speaker 02:
Yes.

[00:21:19] Speaker 02:
So the point here is that at the time of the invention, March 2008, which is the claim priority date for the independent claims which recite the single molecule sequencing term.

[00:21:28] Speaker 03:
So when the question says 2008 to 2009, you're suggesting that excludes March 2008?

[00:21:33] Speaker 02:
No, I'm suggesting that over that range, there may have been a better understanding of the terms single molecule sequencing, but it certainly was not the case.

[00:21:45] Speaker 03:
OK, let's just say hypothetically I don't agree with this.

[00:21:48] Speaker 03:
Move on to your next argument.

[00:21:49] Speaker 01:
So it strikes me that the problem here, as Judge Chen was suggesting, is we seem to have potentially conflicting testimony as to whether there was a well-understood

[00:22:02] Speaker 01:
meaning to single molecule sequencing is including nanopore sequencing in the relevant time period.

[00:22:10] Speaker 01:
What are we to do if we find that the record is conflicting about that?

[00:22:15] Speaker 02:
Well, we have this conflicting testimony as to what was the customary meaning of the term.

[00:22:21] Speaker 02:
And so that is why it is much more important here to refer to the specification to determine how the patentees use the term

[00:22:31] Speaker 02:
in the context of the patent at the time of the invention.

[00:22:35] Speaker 02:
And the specification here of both patents clearly and consistently describe single molecule sequencing as requiring template-dependent synthesis.

[00:22:46] Speaker 02:
Independent claims require single molecule sequencing of a template molecule.

[00:22:52] Speaker 02:
The use of the term template molecule as opposed to merely a molecule suggests that a molecule serves as a template

[00:23:00] Speaker 02:
for generating.

[00:23:01] Speaker 03:
Are you saying you can't use a template molecule through nanopore sequencing?

[00:23:05] Speaker 03:
No.

[00:23:07] Speaker 03:
So that doesn't move the ball in any direction, whether nanopore sequencing is encompassed or not encompassed.

[00:23:14] Speaker 03:
Just the fact that it says a template sequence, a template molecule.

[00:23:18] Speaker 02:
But in nanopore sequencing, as the administrative law judge found, and the parties do not dispute, nanopore sequencing is substantially different

[00:23:29] Speaker 02:
than template-dependent synthesis because it does not involve synthesis of a complementary strand.

[00:23:35] Speaker 02:
So the claim language itself, which suggests synthesis of a template molecule, means that nanopore sequencing would not be encompassing.

[00:23:43] Speaker 03:
Well, you're assuming the conclusion by assuming that something in the claim language itself is driving us towards synthesis.

[00:23:51] Speaker 03:
The real question is whether this inventor did something to truly

[00:23:58] Speaker 03:
constrain and characterize the meaning of single molecule sequencing to be put within the context of synthesis and synthesis only.

[00:24:06] Speaker 03:
That's really the debate here.

[00:24:08] Speaker 02:
Right.

[00:24:09] Speaker 02:
And we're not solely relying on the acclaimed language here.

[00:24:12] Speaker 02:
It simply supports the commission's construction and the inventor's description of their invention in the specification.

[00:24:20] Speaker 01:
What are we to make of the citation to Clark and specification in the part that Mr. Reinus was reading?

[00:24:26] Speaker 02:
The citation to Clark is simply for the purpose of supporting the patent's disclosure of using a nanoforce sensor to detect nucleotides in a synthesized strand that are incorporated into a synthesized strand.

[00:24:42] Speaker 02:
Clark describes a very different process that destroys a DNA strand and does not use labels.

[00:24:50] Speaker 02:
Those disclosures are not referenced at all in the specification.

[00:24:55] Speaker 02:
And moreover, are incompatible with the embodiments described in the specification.

[00:25:01] Speaker 02:
So this notion that the specification refers to nanopore sequencing in Clark is just not there.

[00:25:08] Speaker 02:
There's no mention of nanopore sequencing at all.

[00:25:11] Speaker 03:
Clark doesn't talk about nanopore sequencing?

[00:25:14] Speaker 02:
Yes, it does.

[00:25:15] Speaker 02:
Clark does.

[00:25:16] Speaker 02:
The specification does not.

[00:25:17] Speaker 02:
And it does not do so by simply citing to Clark and stating that

[00:25:24] Speaker 02:
nanopore sensors are used for detecting incorporated nucleotides.

[00:25:29] Speaker 03:
I guess the question is, should the reference to Clark, the citation to Clark, be understood as doing something more than just discussing using a nanopore sequence in the context of synthesis, but in fact is communicating to the reader that the inventor is actually thinking about what Clark is actually disclosing, nanopore sequencing?

[00:25:52] Speaker 02:
I don't believe an inference like that can be made here for claim construction.

[00:25:56] Speaker 02:
We have Clark, which describes a very different invention.

[00:25:59] Speaker 02:
And as this court held in trustees of Columbia, a cited reference that describes a different invention is not relevant to claim construction.

[00:26:08] Speaker 01:
So is the idea here that Clark is cited for the use of nanopore sensors rather than nanopore sequencing?

[00:26:16] Speaker 02:
Yes.

[00:26:19] Speaker 02:
Using the nanopore sensor for detection purposes is different than nanopore sequencing as the particle.

[00:26:25] Speaker 03:
Just curious, how is it different?

[00:26:26] Speaker 03:
I mean, you're feeding a strand through the nanopore sensor, and that sounds like nanopore sequencing.

[00:26:35] Speaker 02:
It is simply pulling the strand to detect a nucleotide to identify what that nucleotide is.

[00:26:44] Speaker 02:
Nanopore sequencing

[00:26:45] Speaker 02:
involves determining the order of a series of nucleotides in a row.

[00:26:50] Speaker 02:
And the prior art, if you look at Gupta Postma-Clark, talks about the difficulty in March 2008.

[00:26:57] Speaker 02:
Actually, those preferences are post-March 2008, but even then, there was difficulty in going to detection.

[00:27:02] Speaker 03:
I'm just trying to understand how Clark is being referred to and used and the mention of its nanopore sensor in column seven.

[00:27:12] Speaker 03:
What's happening in column 7?

[00:27:15] Speaker 03:
Is there a DNA strand being fed through a nanopore sensor?

[00:27:21] Speaker 03:
Or you seem to be suggesting there's just a single base that's being fed through the nanopore sensor.

[00:27:27] Speaker 03:
That doesn't sound right to me.

[00:27:29] Speaker 02:
To understand what column is saying, you simply have to look at what the specification says.

[00:27:35] Speaker 02:
OK, well, help me.

[00:27:36] Speaker 02:
Tell me, what is that?

[00:27:37] Speaker 02:
The paragraph starts off where we had this reference to Clark.

[00:27:41] Speaker 02:
that it will be appreciated that in accordance with the sequencing compositions of the invention, the nucleotides or nucleotide analogs may be detectable by any of a variety of different mechanisms.

[00:27:54] Speaker 02:
And going to that specific sentence with the reference to Clark, likewise, non-optical labels may be employed such as highly charged moieties that may be detected by electrical chemical systems such as, for example, nanopore sensors.

[00:28:09] Speaker 02:
That's it.

[00:28:10] Speaker 02:
No mention of nanopore sequencing and what it takes.

[00:28:13] Speaker 03:
Can you just translate to me for me?

[00:28:15] Speaker 03:
I understand what those words are, but what are they teaching us?

[00:28:20] Speaker 03:
Are you feeding a DNA strand through a nanopore sensor?

[00:28:23] Speaker 02:
It says that they're using a nanopore sensor to detect the nucleotides that are going through the nanopore.

[00:28:32] Speaker 02:
That's just one step.

[00:28:33] Speaker 03:
Why isn't that nanopore sequencing?

[00:28:35] Speaker 02:
because detection is simply one step of the sequencing process.

[00:28:39] Speaker 02:
There are other steps to it.

[00:28:40] Speaker 03:
What else is going on in nanopore sequencing other than the act of running a DNA strand through the sensor and then identifying the individual bases?

[00:28:51] Speaker 02:
You need to pull the strand to the next nucleotide and detect that nucleotide and do that over and over again to get a sequence, the identification of a number of nucleotides in a row.

[00:29:02] Speaker 02:
Just detecting one nucleotide does not get you a

[00:29:04] Speaker 02:
get you a sequence.

[00:29:06] Speaker 02:
And the prior art talks about the difficulties from going from detection to sequencing.

[00:29:10] Speaker 03:
Okay, so your position is, column seven is only about feeding a single nucleotide into the sensor.

[00:29:15] Speaker 03:
That's correct.

[00:29:16] Speaker 03:
That's what you get.

[00:29:16] Speaker 02:
For detection purposes only.

[00:29:20] Speaker 01:
Okay, let's hear from Mr. Hayes.

[00:29:21] Speaker 01:
Thank you.

[00:29:24] Speaker 01:
No, not yet, Mr. Ryan.

[00:29:29] Speaker 01:
Nice try, Mr. Ryan.

[00:29:36] Speaker 05:
Good morning, Stephen Hasch on behalf of other engineers at Oxford Nanopore.

[00:29:39] Speaker 05:
If I could address Judge Chin's issue, your last question to Mr. Reines was... Well, how about my last question to your co-counsel over there?

[00:29:49] Speaker 03:
Okay.

[00:29:50] Speaker 03:
Column 7, it's just a single nucleotide that's being fed through that nanopore sensor in column 7?

[00:29:55] Speaker 05:
No, no, no.

[00:29:56] Speaker 05:
Column 7 is about... Column 7 talks about labels and how to detect labels, non-optical labels.

[00:30:04] Speaker 05:
And so, and it says the way you detect non-optical labels is by chem-fet or nanopore sensors.

[00:30:10] Speaker 05:
For example, chem-fet or nanopore sensors.

[00:30:13] Speaker 05:
Your question about labels is very pertinent to that.

[00:30:16] Speaker 05:
Labels are only used in synthetic processes.

[00:30:19] Speaker 03:
Paint for me a picture of what's happening with the nanopore sensor from Clark in the context of column 7.

[00:30:25] Speaker 03:
What is being fed through the sensor?

[00:30:27] Speaker 03:
Precisely.

[00:30:28] Speaker 03:
Clark doesn't, doesn't.

[00:30:30] Speaker 05:
use labels, it only talks about sensors.

[00:30:32] Speaker 03:
No, I'm asking you to paint a picture for me.

[00:30:34] Speaker 03:
What is happening when you use the nanopore sensor in Clark?

[00:30:38] Speaker 03:
What is the specification telling us?

[00:30:40] Speaker 05:
But you're conflating Clark and nanopore sensors.

[00:30:42] Speaker 05:
The sentence is optical labels, non-optical labels can be used with nanopore sensors.

[00:30:49] Speaker 05:
Clark doesn't talk about labeled nucleotides.

[00:30:54] Speaker 05:
Clark is a destructive process.

[00:30:57] Speaker 05:
The labels aren't nucleotide.

[00:30:58] Speaker 05:
The citation is solely for the purpose that Clark discloses nanopore sensors.

[00:31:05] Speaker 05:
It doesn't talk about detecting labeled nucleotides.

[00:31:08] Speaker 05:
That is just the patent.

[00:31:10] Speaker 05:
And to your question, labels are only used in synthetic processes.

[00:31:15] Speaker 05:
The purpose of synthesis with the polymerase is you incorporate a labeled nucleotide.

[00:31:19] Speaker 03:
Well, now that takes me to the question of why did the patent

[00:31:24] Speaker 03:
refer to Clark and Clark's nanopore sensor.

[00:31:27] Speaker 03:
Yeah, there has to be something we take away from it.

[00:31:29] Speaker 05:
What is it?

[00:31:30] Speaker 05:
It's a simple citation to the use of nanopores as sensors.

[00:31:35] Speaker 05:
For what purpose?

[00:31:37] Speaker 03:
To detect.

[00:31:37] Speaker 05:
In the context of this patent.

[00:31:39] Speaker 05:
To detect something.

[00:31:41] Speaker 05:
Here, what they're talking about is detecting labels.

[00:31:44] Speaker 01:
What's a label?

[00:31:45] Speaker 05:
A label is something that you put on a nucleotide.

[00:31:48] Speaker 05:
And when it is incorporated into the growing strand by a polymerase,

[00:31:51] Speaker 05:
that label does something.

[00:31:53] Speaker 05:
In the context of a fluorescent label, the label is cleaved off and there's a little flash of light.

[00:31:59] Speaker 05:
And so that's what everything before is talking about.

[00:32:03] Speaker 05:
As Mr. Reynes, as PacBio admitted at the Markman hearing, the only embodiments, he gave us credit for this.

[00:32:11] Speaker 05:
Our argument is the only embodiments, the only thing that's disclosing this patent, the present invention language, every embodiment, every example, not just the smart sequencing,

[00:32:21] Speaker 05:
Everything is synthetic.

[00:32:23] Speaker 05:
There is no disclosure of nonsynthetic processes.

[00:32:26] Speaker 05:
When you look at the sentence, it's context dependent.

[00:32:29] Speaker 01:
So you're saying that the nanopore sensors are used here as part of a synthetic process?

[00:32:35] Speaker 05:
Yes, Your Honor.

[00:32:36] Speaker 05:
That's exactly correct.

[00:32:37] Speaker 05:
And that question was asked of Dr. Ehrlich, who is there.

[00:32:41] Speaker 03:
I thought you answered my question by saying, no, you can't use a nanopore sensor with a synthetic process.

[00:32:47] Speaker 05:
No, you can use a non-

[00:32:49] Speaker 05:
Clark doesn't use the nanopore sensor in a synthetic process.

[00:32:53] Speaker 05:
This patent contemplates the use of labels.

[00:32:57] Speaker 05:
And the only reason you use labels is because of a synthetic process.

[00:33:01] Speaker 03:
OK, so explain to me how this patent uses a nanopore sensor in a synthetic process.

[00:33:06] Speaker 03:
What are you actually doing?

[00:33:08] Speaker 05:
So what it's contemplating is the synthesis of a strand with labeled nucleotides.

[00:33:14] Speaker 05:
So the polymerase is synthesizing the strand and incorporating the labeled nucleotides.

[00:33:18] Speaker 05:
They use non-optical labels like a metal or a molecule that has a specific signal when it goes through the nanopore.

[00:33:26] Speaker 05:
Because the nanopore just detects differences in current.

[00:33:30] Speaker 01:
So you're using the sensor to determine what the label says?

[00:33:33] Speaker 05:
You're using the sensor to detect what the label is.

[00:33:36] Speaker 05:
And so a G will have a label on it that creates a specific signal.

[00:33:42] Speaker 05:
A T will have a label on it that creates a specific signal.

[00:33:44] Speaker 05:
And the label is on the end of the snippet?

[00:33:47] Speaker 05:
is on the nucleotide.

[00:33:48] Speaker 05:
So the polymerase is just making a copy.

[00:33:52] Speaker 05:
And that's what, as Ms.

[00:33:53] Speaker 05:
Noyle was talking to you, the template.

[00:33:56] Speaker 05:
The template here, the claim talks about a template.

[00:33:59] Speaker 05:
A template is something that is copied.

[00:34:02] Speaker 05:
And so the claims use of the word template is very relevant here.

[00:34:05] Speaker 05:
Because when you talk about a synthetic process, you're talking about synthesis, you're making a copy.

[00:34:11] Speaker 05:
And so the language of the claim gets this idea of,

[00:34:15] Speaker 05:
You're taking a DNA strand and making the whole DNA strand into a template by adding that linker on, which creates just one issue that I want to just address.

[00:34:25] Speaker 05:
Mr. Ranis makes the argument that that template is somehow novel, that nobody ever thought about that.

[00:34:29] Speaker 05:
People have been using that type of template for decades.

[00:34:35] Speaker 05:
It is not something new.

[00:34:36] Speaker 05:
It is not something not obvious.

[00:34:37] Speaker 05:
Wait, you're talking about the hairpin?

[00:34:39] Speaker 05:
The hairpin.

[00:34:40] Speaker 05:
Put annealing hairpins onto DNA structures.

[00:34:43] Speaker 05:
His attorney argued that that template is somehow novel, not obvious.

[00:34:47] Speaker 05:
That's been around for generations.

[00:34:50] Speaker 05:
Frederick Sanger, in his Nobel speech, said, you want to sequence both strands.

[00:34:55] Speaker 05:
It's accepting the Nobel Prize for DNA sequencing.

[00:34:59] Speaker 05:
Is this in the record?

[00:35:01] Speaker 05:
Is this in the record?

[00:35:03] Speaker 05:
I'm not sure it's in the record.

[00:35:04] Speaker 05:
OK.

[00:35:07] Speaker 05:
I mean, this is not a jury box over here.

[00:35:10] Speaker 05:
Sure.

[00:35:11] Speaker 05:
These structures are not novel.

[00:35:12] Speaker 05:
They're not new.

[00:35:13] Speaker 05:
They're not obvious.

[00:35:14] Speaker 05:
There isn't any great innovation here.

[00:35:16] Speaker 05:
This is a new argument.

[00:35:17] Speaker 03:
OK, you're now trying to make an invalidity analysis here.

[00:35:21] Speaker 03:
We're trying to understand how to understand the meaning of single molecule sequencing.

[00:35:27] Speaker 05:
But your point is to continue with a sensor.

[00:35:30] Speaker 05:
The sensor would detect whatever that label is.

[00:35:34] Speaker 05:
It is a molecule that is going to create a specific

[00:35:40] Speaker 05:
change in the current as it is synthesized and progresses through the nanopore sensor.

[00:35:46] Speaker 05:
And so that label is going to, for the nucleotides as they're incorporated, because each nucleotide as it's incorporated is going to have a different label on it.

[00:35:55] Speaker 05:
The G's will have one label, the T's will have one label, the C's will have one label, and the A's will have one label.

[00:36:00] Speaker 05:
And as the synthesis is created and as those nucleotides are added into the strand and it progresses through the nanopore,

[00:36:06] Speaker 05:
According to what the patent is saying or contemplating, you'll get a different signal.

[00:36:12] Speaker 05:
But that is a synthetic process.

[00:36:14] Speaker 05:
The context of those statements, Mr. Reines' argument that the patent contemplates is anything but synthetic is wrong.

[00:36:24] Speaker 05:
He conceded that at the Markman hearing.

[00:36:26] Speaker 01:
OK, but what about your expert's testimony about the meaning of single molecule sequencing?

[00:36:34] Speaker 05:
I think that was made an error, and it isn't specific to the time frame we're talking about here of 2008.

[00:36:40] Speaker 05:
It spans through 2009.

[00:36:42] Speaker 06:
Were you at that deposition?

[00:36:46] Speaker 05:
At the Goldman deposition?

[00:36:48] Speaker 05:
Yeah.

[00:36:48] Speaker 05:
I was not.

[00:36:49] Speaker 05:
I was at the Ehrlich deposition, and I asked the question.

[00:36:51] Speaker 06:
Yeah.

[00:36:52] Speaker 06:
I'm just wondering why somebody didn't say objection, foundation, vague, ambiguous, et cetera, et cetera.

[00:36:58] Speaker 03:
I will talk to the person who yielded the deposition about that.

[00:37:02] Speaker 03:
You're asking us to not give credit to your own expert's testimony that at the time frame of 2008-2009, single molecule sequencing encompassed nanopore sequencing?

[00:37:13] Speaker 05:
But it is time frame dependent.

[00:37:14] Speaker 05:
And it's 2008, not 2008 through 2009.

[00:37:18] Speaker 03:
As Dr. Ehrlich was saying... I guess you're saying 2008-2009 doesn't encompass March 2008?

[00:37:25] Speaker 05:
But it also encompasses December 2009.

[00:37:28] Speaker 05:
And by December 2009... Right.

[00:37:30] Speaker 03:
What if it said 2008-2018?

[00:37:32] Speaker 03:
It's ambiguous.

[00:37:34] Speaker 01:
Well, suppose we disagree with that.

[00:37:36] Speaker 01:
Suppose we think that there's a real conflict here in the testimony.

[00:37:40] Speaker 05:
I think that the record as a whole is not as doctor... I mean, it's not as Mr. Reyna says.

[00:37:47] Speaker 05:
There's a great deal of conflict.

[00:37:48] Speaker 05:
And I think that there's deference that should be accorded in the factual determination that was made by

[00:37:53] Speaker 05:
the commission here.

[00:37:56] Speaker 05:
They looked at the record as a whole, and you look at the references that are cited by PacBio.

[00:38:03] Speaker 05:
That's seven references out of the thousands of references that talk about DNA sequencing, and they cherry pick them.

[00:38:08] Speaker 01:
And the fact is... Well, we don't give deference to them to the extent that they're interpreting the intrinsic evidence, only the extrinsic evidence.

[00:38:16] Speaker 01:
I'm not sure that there's a finding here by the ITC about the extrinsic evidence.

[00:38:24] Speaker 05:
They, packed by this argument, is that the Planned and Ordinary Meaning controls, that the extrinsic evidence dictates this Planned and Ordinary Meaning.

[00:38:33] Speaker 05:
It's a very Texas digital-esque argument.

[00:38:35] Speaker 05:
And I think what's illustrative, if we look at the cases, is a case like Nystrom, where the court in pre-Nystrom, pre-Phillips in Nystrom, looked at a dictionary definition, looked at extrinsic evidence, and said a board is wood and other materials based upon

[00:38:53] Speaker 05:
the extrinsic definition of what a board is.

[00:38:58] Speaker 05:
That was contrary to what the patent said, what all the embodiments were, what the present invention language.

[00:39:04] Speaker 05:
Post Phillips, the Nystrom court came back and said, Phillips dictates that we look at the specification.

[00:39:12] Speaker 05:
The specification is the single best guide.

[00:39:15] Speaker 05:
They've acknowledged that there is not a single embodiment.

[00:39:18] Speaker 05:
The present invention language here is unequivocal.

[00:39:22] Speaker 05:
Mr. Reines acknowledged that the present invention language talks about nothing more than template-dependent processes.

[00:39:28] Speaker 03:
So what statement in the specification disavows or disclaims anything other than synthesis?

[00:39:35] Speaker 05:
As the court in Regence said, we believe that the language, the present invention language, the repeated present invention language rises to the level of a disavow.

[00:39:44] Speaker 05:
But the court didn't need to get to a disavow.

[00:39:47] Speaker 05:
As the court in Regence of Columbia University said,

[00:39:51] Speaker 05:
a disavowal, when the specification makes it clear that this is what the invention is, that you don't need an express disavowal, you don't need a disclaimer.

[00:39:59] Speaker 03:
It doesn't have to be an express, it can be implied.

[00:40:01] Speaker 03:
That's fine, but what is the evidence here?

[00:40:05] Speaker 05:
The evidence is repeated characterization of the invention.

[00:40:09] Speaker 05:
All the embodiments are consistent with this.

[00:40:12] Speaker 05:
A person of ordinary skill in the art cannot read this specification and believe

[00:40:18] Speaker 05:
that the invention that's being described is anything more than an application of a well-known template in template-dependent processes.

[00:40:29] Speaker 05:
As retractable technology said, the claimed scope is tethered to the specification.

[00:40:35] Speaker 05:
There is no reading of this specification, contrary to this revisionist argument that Mr. Reines is making now.

[00:40:42] Speaker 05:
As he said, all of the embodiments, every single one, the general and particular language,

[00:40:48] Speaker 05:
The primary embodiments, the other embodiments, all of the examples are template-dependent synthesis.

[00:40:55] Speaker 05:
OK.

[00:40:55] Speaker 05:
I think we're out of time.

[00:40:57] Speaker 05:
Thank you, Mr. Hasch.

[00:41:02] Speaker 04:
I'd like to just clarify my response to Judge Dyke.

[00:41:06] Speaker 04:
The Turner Declaration, which is submitted multiple times, refers to GUPTA, goes through the history of DNA sequencing, says, GUPTA provides a review specifically describing the various single molecule sequencing approaches in 2008.

[00:41:18] Speaker 04:
which include helicos, PacBio, and nanopore sequencing.

[00:41:21] Speaker 04:
And he does.

[00:41:22] Speaker 04:
And he says nanopore sequencing is single molecule sequencing.

[00:41:25] Speaker 04:
It's not a vague thing.

[00:41:26] Speaker 04:
And then he said, then after analyzing the literature, he says, thus is described above the term single molecule sequence as well understood in the field at the time of the invention to mean carrying out and states it.

[00:41:38] Speaker 04:
So the evidence of the standard usage is the square admission of their own expert, the declarations

[00:41:46] Speaker 04:
documented with prior art.

[00:41:48] Speaker 04:
Every prior art reference, we put seven in extrinsic and then the two intrinsic.

[00:41:53] Speaker 04:
And they use single molecule sequencing with respect to it.

[00:41:56] Speaker 04:
Now getting to Judge Dyke, I think the ultimate point here is the IDC punted on actually facing what the plain meaning was.

[00:42:04] Speaker 04:
They just kind of went through and then cited this really, I think, unfair statement from Dr. Erlich about errors in it and commercialization.

[00:42:13] Speaker 04:
to overcome all of that and says, well, therefore VUDU, in a whole, we find that extrinsic evidence doesn't support us, which is a vague statement.

[00:42:21] Speaker 04:
It doesn't grapple with the plain meaning in the field, which I think is a critical bedrock.

[00:42:26] Speaker 04:
On the actual specification itself, I want to make two points.

[00:42:30] Speaker 04:
The first point is everything that Mr. Hash said about how you can have synthesis with nanopore sequencing isn't consistent with that same body of evidence that I just gave you, which you can go through or have your clerks go through.

[00:42:41] Speaker 04:
Satin adipose sequencing has always been non-synthesis.

[00:42:45] Speaker 04:
So his story of how you might do it is based on nothing at all.

[00:42:51] Speaker 04:
The other thing I want to say is if you go to column 9 and 10, there's a bridge of 9 and 10, it describes this concept of the hairpin invention.

[00:43:00] Speaker 04:
And it describes it.

[00:43:01] Speaker 04:
And it doesn't have anything to do with synthesis.

[00:43:03] Speaker 04:
It goes through and it says, you take one, you take the other, you put it in between, and then you can do them both at the same time.

[00:43:09] Speaker 04:
It doesn't care how it goes through the sensor and what happens.

[00:43:12] Speaker 04:
And so that's the part.

[00:43:14] Speaker 04:
To me, it's an omnibus specification.

[00:43:18] Speaker 04:
And to say, well, a lot of stuff's about synthesis.

[00:43:21] Speaker 04:
Therefore, this aspect of it, which is synthesis independent, has to be limited when the claim scope isn't that way and that wasn't how it issued.

[00:43:29] Speaker 04:
It just doesn't seem like how we should be doing this.

[00:43:31] Speaker 04:
Especially since people rely on the captive of the claims.

[00:43:35] Speaker 01:
Okay.

[00:43:36] Speaker 04:
Thank you very much.

[00:43:37] Speaker 04:
Thank you both.

[00:43:38] Speaker 04:
Thank you all counsel cases submitted.