Page 1
`
` UNITED STATES PATENT AND TRADEMARK OFFICE
` BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
` SEQUENOM, INC.,
` Petitioner,
` vs. No. IPR2013-00390
` Patent 8,195,415
` THE BOARD OF TRUSTEES OF THE
` LELAND STANFORD JUNIOR
` UNIVERSITY,
` Patent Owner.
` ____________________________/
`
`HEI-MUN CHRISTINA FAN and
`STEPHEN QUAKE,
` Junior Party,
` vs. No. 105,922 (DK)
` (Technology Center 1600)
`YUK-MING DENNIS LO, ROSSA WAI
`KWUN CHIU, and KWAN CHEE CHAN,
`
` Senior Party.
`____________________________/
`
` Videotaped Cross-Examination of
`
` HEI-MUN CHRISTINA FAN, PH.D.
`
` Redwood City, California
`
` Wednesday, June 25, 2014
`
` Veritext Legal Solutions
` Mid-Atlantic Region
` 1250 Eye Street NW - Suite 1201
` Washington, D.C. 20005
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`SEQUENOM EXHIBIT 1089
`Sequenom v. Stanford
`IPR2013-00390
`
`VERITEXT NATIONAL COURT REPORTING COMPANY
`215-241-1000 ~ 610-434-8588 ~ 302-571-0510 ~ 202-803-8830
`SEQUENOM EXHIBIT 1089
`
`
`
` UNITED STATES PATENT AND TRADEMARK OFFICE
` BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
` SEQUENOM, INC.,
` Petitioner,
` vs. No. IPR2013-00390
` Patent 8,195,415
` THE BOARD OF TRUSTEES OF THE
` LELAND STANFORD JUNIOR
` UNIVERSITY,
` Patent Owner.
` ____________________________/
`
`HEI-MUN CHRISTINA FAN and
`STEPHEN QUAKE,
` Junior Party,
` vs. No. 105,922 (DK)
` (Technology Center 1600)
`YUK-MING DENNIS LO, ROSSA WAI
`KWUN CHIU, and KWAN CHEE CHAN,
`
` Senior Party.
`____________________________/
`
` Videotaped Cross-Examination of
`
` HEI-MUN CHRISTINA FAN, PH.D.
`
` Redwood City, California
`
` Wednesday, June 25, 2014
`
` Veritext Legal Solutions
` Mid-Atlantic Region
` 1250 Eye Street NW - Suite 1201
` Washington, D.C. 20005
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`SEQUENOM EXHIBIT 1089
`Sequenom v. Stanford
`IPR2013-00390
`
`VERITEXT NATIONAL COURT REPORTING COMPANY
`215-241-1000 ~ 610-434-8588 ~ 302-571-0510 ~ 202-803-8830
`SEQUENOM EXHIBIT 1089
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` UNITED STATES PATENT AND TRADEMARK OFFICE
` BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`Page 2
`
` SEQUENOM, INC.,
`
` Petitioner,
`
` vs. No. IPR2013-00390
` Patent 8,195,415
` THE BOARD OF TRUSTEES OF THE
` LELAND STANFORD JUNIOR
` UNIVERSITY,
`
` Patent Owner.
` ____________________________/
`HEI-MUN CHRISTINA FAN and
`STEPHEN QUAKE,
`
` Junior Party,
`
` vs. No. 105,922 (DK)
` (Technology Center 1600)
`YUK-MING DENNIS LO, ROSSA WAI
`KWUN CHIU, and KWAN CHEE CHAN,
` Senior Party.
`____________________________/
`
` Videotaped deposition of HEI-MUN CHRISTINA FAN,
`PH.D., taken at the offices of Weil, Gotshal & Manges
`LLP, 201 Redwood Shores Parkway, Redwood Shores,
`California, beginning at 10:02 A.M. and ending at
`P.M., on Wednesday, June 25, 2014, before Leslie
`Rockwood, RPR, CSR No. 3462.
`
`VERITEXT NATIONAL COURT REPORTING COMPANY
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`
`
`APPEARANCES OF COUNSEL:
`
`Page 3
`
`FOR THE PETITIONER SEQUENOM, INC., AND YUK-MING
`
`DENNIS LO:
`
` PERKINS COIE LLP
`
` BY: MICHAEL J. WISE, ESQ.
`
` 1888 Century Park East, Suite 1700
`
` Los Angeles, California 90067-1721
`
` (310) 788-3210
`
` MWise@perkinscoie.com
`
`FOR THE PATENT OWNER THE BOARD OF TRUSTEE OF THE LELAND
`
`STANFORD JUNIOR UNIVERSITY:
`
` ROTHWELL, FIGG, ERNST & MANBECK, PC
`
` BY: R. DANNY HUNTINGTON, ESQ.
`
` BY: SETH E. COCKRUM, PH.D., ESQ.
`
` 607 14th Street, N.W., Suite 800
`
` Washington, DC 20005
`
` (202) 783-6040
`
` dhuntington@rfem.com
`
` scockrum@rfem.com
`
`Also Present:
`
` Marcus Burch, Illumina (via speakerphone)
`
` Sean Grant, Videographer
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`Page 4
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` I N D E X
`
`WEDNESDAY, JUNE 25, 2014
`
`WITNESS EXAMINATION
`
`HEI-MUN CHRISTINA FAN, PH.D.
`
` BY MR. WISE 8,
`
`QUESTIONS WITNESS INSTRUCTED NOT TO ANSWER:
`
` Page Line
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`Page 5
`
` DEPOSITION EXHIBITS
`
` HEI-MUN CHRISTINA FAN, PH.D.
`
`NUMBER DESCRIPTION IDENTIFIED
`
`Exhibit 1100 Fan Priority Statement, 48
`
` 7/31/13
`
`Exhibit 1101 Initial Sequencing and 103
`
` Analysis of the Human Genome,
`
` 2/15/01
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` Wednesday, June 25, 2014; Redwood Road, California
`
` 10:02 A.M.
`
`Page 6
`
` PROCEEDINGS
`
` THE VIDEOGRAPHER: Good morning. We're on the
`
`record. The time is 10:02 a.m. The date is June 25th,
`
`2014. This begins the videotaped deposition of
`
`Christina Fan, Ph.D.
`
` My name is Sean Grant, here with our court
`
`reporter Leslie Rockwood. We're here from Veritext Legal
`
`Solutions at the request of counsel for petitioner.
`
` This deposition is being held at Weil, Gotshal &
`
`Manges LLP in Redwood Shores, California. The caption of
`
`this case is Sequenom, Inc., Petitioner versus the Board
`
`of Trustees of the Leland Stanford Junior University,
`
`Patent Owner, Case Number IPR2013-00390, Patent
`
`8,195,495, and Junior Party Fan versus Senior Party Lo,
`
`Patent Inference Number 105,922, Technology Center 1600.
`
`Both are filed in the United States Patent and Trademark
`
`Office before the Patent Trial and Appeal Board.
`
` Please note that audio and video recording will
`
`take place unless all parties have agreed to go off the
`
`record. Microphones are sensitive and may pick up
`
`whispers, private conversations or cellular interference.
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` At this time will all present please identify
`
`themselves for the record, beginning with the witness.
`
`Page 7
`
` Your name, please.
`
` THE WITNESS: Christina Fan.
`
` THE VIDEOGRAPHER: Thank you.
`
` MR. HUNTINGTON: I'm Danny Huntington, and I
`
`have with me Seth Cockrum. We're for the patent owner.
`
` MR. WISE: I'm Michael Wise. I represent party
`
`Sequenom in the IPR and Party Lo in the interference.
`
` (Interruption in proceedings.)
`
` THE VIDEOGRAPHER: Will the Certified Court
`
`Reporter please swear in the witness.
`
` MR. WISE: Before you do that, let's just note
`
`for the record that Mr. Huntington's going to dial in
`
`Marcus Burch.
`
` MR. HUNTINGTON: Yes.
`
` MR. WISE: And he's from?
`
` MR. HUNTINGTON: He works for Illumina.
`
` MR. WISE: Oh, Illumina. Okay. Thank you.
`
` (Interruption in proceedings.)
`
` THE VIDEOGRAPHER: Will the Certified Court
`
`Reporter please swear in the witness.
`
` THE REPORTER: If you'd raise your right hand,
`
`please.
`
` You do solemnly state that the evidence you
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`Page 8
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`shall give in this matter shall be the truth, the whole
`
`truth and nothing but the truth, so help you God?
`
` THE WITNESS: Yes.
`
` THE REPORTER: Thank you.
`
` THE VIDEOGRAPHER: Counsel, you may proceed.
`
` MR. WISE: Thank you.
`
` EXAMINATION
`
`BY MR. WISE:
`
` Q. Good morning.
`
` A. Good morning.
`
` Q. Have you ever been deposed before?
`
` A. I have been deposed before.
`
` Q. How many times?
`
` A. Once.
`
` Q. In the litigation for -- between Illumina and
`
`Sequenom?
`
` A. I believe it is Verinata against Sequenom.
`
` Q. Okay. Well, let me run through some of the
`
`rules for you here. At the -- I'm required for the
`
`interference piece to give you this instruction at the
`
`beginning of the deposition:
`
` "At the beginning of a cross-examination, the
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`party conducting the cross-examination must instruct the
`
`witness on the record to ask deposing counsel," that's
`
`me, "rather than the witness' own counsel," that's
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`Mr. Huntington, "for clarifications, definitions or
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`explanations of any words, questions or documents
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`presented during the cross-examination. The witness must
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`Page 9
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`follow these instructions."
`
` Will you do that for us today?
`
` A. I understand, yes.
`
` Q. Thank you.
`
` Now, you've been given -- put under oath, the
`
`same type of oath you'd be given if you were testifying
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`live at trial, and kind of the concept is rather than
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`having you in front of a judge right now, the Board of
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`Patents Appeals and Interferences conducts this type of a
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`trial by paper. So this is the same as giving trial
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`testimony. It's the same oath.
`
` Do you understand that?
`
` A. I understand.
`
` Q. Okay. At the end of this proceeding, and I
`
`suspect at the end of your last deposition, you'll be
`
`given a transcript that you can review to make changes
`
`and make corrections. And if you go beyond, kind of,
`
`normal grammatical or somebody misheard and there's a
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`misspelling types of changes, we'll have an opportunity
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`to comment on those changes. You know, for example if
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`you change a word from "yes" to "no," our side of the
`
`equation or our side of the table will be saying your
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`Page 10
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`testimony's not credible for changing testimony like
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`that.
`
` So will you do your best to give us your best
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`testimony today and, you know, be very clear with what
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`you're saying and spell out words that might -- the court
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`reporter might not be able to know off the top of her
`
`head? Will you do that for us today?
`
` A. Yes.
`
` Q. Okay. We need verbal responses. Even though we
`
`have a videographer here, it's highly likely that the
`
`Board's going to be reading the transcript as opposed to
`
`watching the video, as exciting as it may be. So we need
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`you to give yes-and-no answers as opposed to nods of the
`
`head or shaking of the head.
`
` Will you do that for us today?
`
` A. I understand.
`
` Q. Okay. Next one, I don't think we'll have too
`
`much of this, but a lot of -- sometimes in depositions
`
`I'll ask a question and then the defending attorney will
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`object, so it's important during the flow of this --
`
`because the lady over here trying to transcribe
`
`everything can't transcribe if more than one person is
`
`speaking at the same time. So ideally, I ask a question,
`
`you wait until I'm finished. If Mr. Huntington has an
`
`objection, he states it, and then you answer the
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`Page 11
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`question.
`
` Will you do that for us today?
`
` A. Yes.
`
` Q. Okay. If you need a break for any reason
`
`whatsoever, I'm happy to give them to you. The only
`
`limitation on a break is unless you've been instructed
`
`not to answer a question on the basis of attorney-client
`
`privilege, I ask that you not take a break while the
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`question is pending.
`
` Will you do that for me today?
`
` A. Yes.
`
` Q. Okay. And last but not least, is there any
`
`reason -- are you on any kind of a medication that would
`
`prevent you from testifying truthfully today?
`
` A. No.
`
` Q. Great. All right.
`
` What did you bring with us today -- or with
`
`yourself today or for us today?
`
` A. This is a notebook that was prepared by
`
`attorneys that has the declaration and the accompanying
`
`exhibits.
`
` Q. Is any of it marked up? In other words, are
`
`they clean copies, or do you have any --
`
` A. I believe there were handwritten corrections in
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`the declaration.
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` Q. Okay.
`
` A. And besides that, I don't think so.
`
` MR. HUNTINGTON: Michael, yesterday we sent you
`
`a marked up copy of some changes that Dr. Fan found, and
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`those are in the declaration she has in front of -- in
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`her hand.
`
` MR. WISE: Sure. I don't have any problem with
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`her working off of this set. I'm just trying to figure
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`out if it's marked up in any other way that I, actually,
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`kind of, need to look at it, like when we did debtors.
`
` MR. HUNTINGTON: It is not. The only thing that
`
`I would say is we sent you versions of 2109 and 2010 that
`
`had some missing pages, and we sent you a version with
`
`the missing pages. So what she has in her notebook is
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`she has the full copy on top. Then there's a red tab,
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`and the original version is below that so that she has
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`both.
`
` MR. WISE: That's fine.
`
` MR. HUNTINGTON: But that's all. Other than
`
`that, no other markings.
`
` MR. WISE: That's fine. It will just save me a
`
`lot of time pulling out a lot of exhibits. That's what
`
`I'm trying to establish.
`
` MR. HUNTINGTON: Yes.
`
` MR. WISE: Okay. So your representation to me
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`Page 13
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`is that -- is just what it was, and I can rely on that
`
`and not have to bother giving her extra copies of
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`exhibits that have already been marked?
`
` MR. HUNTINGTON: Agreed.
`
` MR. WISE: Okay. All right. We just saved a
`
`bunch of time. We'll get you out of here earlier.
`
` Q. So let's look at your declaration.
`
` In paragraph 3, if -- you can look at it or not.
`
`It's a pretty simple question. You had a recent change
`
`in position?
`
` A. Correct.
`
` Q. Can you explain to me what happened?
`
` A. So I was -- I'm currently a scientist at
`
`Cellular Research.
`
` Q. Uh-huh.
`
` A. I joined the company in March last year, and
`
`previously I was a scientist at ImmunoMetrix.
`
` Q. I guess what caught my attention is the
`
`difference in titled. You know, at ImmunoMetrix, you
`
`were director of technology, and now you're a staff
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`scientist at Cellular Research. Why'd you change?
`
` A. Well, the title was given by the employer, and
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`it -- I mean, I don't know why there is a difference. I
`
`mean --
`
` Q. Sorry. You know, let me just explain. Maybe
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`it's helpful. Director of technology, you know, is --
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`seems to -- my perception of director of technology is,
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`kind of, a higher, kind of, management level position
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`than a staff scientist. So I'm trying to understand why
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`you would leave that position to go become a staff
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`scientist.
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` A. Actually, both companies are start-up companies,
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`and so the titles sometimes can be -- I mean, it's a
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`little bit arbitrary, depending on how big the company
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`is. And the reason that I left ImmunoMetrix was because
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`it was running into some financial problem, and -- and it
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`was also something to do with the Visa that I have at
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`that time.
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` Q. Okay. Let's push on to paragraph 4, and --
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`actually, paragraph 5. Take a moment to read them,
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`because I'm going to ask you about the terms that are
`
`being used there.
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` A. Okay.
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` Q. Okay. What's your understanding of the
`
`definition of "conception"?
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` A. As I understand it, the conception is when we
`
`first have the idea of the invention.
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` Q. And the idea of the invention being defined as?
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`Let me -- let me -- instead of making that, kind of,
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`open-ended and confusing, if we look at your definition
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`for "reduction to practice," it talks about constructing
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`an embodiment and performing a process meeting every
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`limitation of the interference count.
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` Is it your understanding that for a conception
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`you have to have the idea of every limitation of the
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`interference count?
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` A. Well, I guess I -- well, I don't -- you're
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`talking about conception here --
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` Q. Correct.
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` A. -- or reduction of practice?
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` Q. Okay. When I said before conception of what,
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`you gave me a look, and I realized it's kind of an unfair
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`question. So if we're talking about conception of the
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`count -- and if you'd like, the count is the next -- is
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`on page 8. When you say conception of the count, does
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`that mean each and every limitation of the count?
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` A. When you say "limitation of the count," can you
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`clarify it?
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` Q. Yes, I can. So if we look at paragraph 8.
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` A. Uh-huh.
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` Q. You have the sequencing step, which is the
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`limitation of the count.
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` A. Uh-huh.
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` Q. You have -- I'd call it the alignment step,
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`step B, would you agree with me?
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` A. Yes, I agree.
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` Q. Okay. I would consider that to be a step of the
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`count. Then the determining step, that's a limitation of
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`the count, and then using the values, that's a limitation
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`of the count. So all of these are limitations of the
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`count, so A, B, C and D.
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` A. So can I clarify that what you mean is that when
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`we first conceived the idea, that we actually already
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`have all these steps in mind, that these are the
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`requirement for the invention?
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` Q. Well, I'm trying to understand what -- when you
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`use the word "conception" in your declaration, do you
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`mean all these steps or something less than these steps?
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` A. All these steps.
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` Q. All these steps. Okay. Fair enough.
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` Now, if you, kind of, push forward in your -- if
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`you push forward in your declaration, and I'm not
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`necessarily focusing on any particular date, but, for
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`example, if you look at paragraph 14, 15, 16 and onward,
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`you know, starting at 14 all the way through, say, 29,
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`for example, even 30 and beyond, there's a lot of date
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`specific testimony on particular dates. April 1st, April
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`11th and 28, 29, January 29th on paragraph 19, and so
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`forth, and then if we start at the beginning where I
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`started, paragraph 14, January 2nd.
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` Do you see those dates?
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` A. I do see them.
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` Q. Okay. How did you determine those dates in
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`preparing your declaration?
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` A. So I -- during my stay at the Quake lab, I kept
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`a written lab notebook, a series of lab notebooks, and a
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`lot of the paragraphs here that refer to specific dates,
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`they were taken from the lab notebooks, and also there
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`were paragraphs talking about emails, and so the dates
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`were taken from the emails.
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` Q. Now, you -- if you didn't have those
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`documentation -- that documentation, would you be able to
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`construct those dates with that kind of accuracy?
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` A. I would not be able to say, like, that specific
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`date.
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` Q. Right.
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` A. But maybe around, like, to the month --
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` Q. Okay.
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` A. -- two months or something like that.
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` Q. Sure. Understood.
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` Now, other than where you've referenced a
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`particular exhibit, you know, you say, "On January 2nd, I
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`did this," and then you cite to a particular exhibit, be
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`it your notebook or an email, do you rely on your memory
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`to construct the rest of the events?
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` A. For everything that we -- that I have in here,
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`they're literally facts that were drawn from either the
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`notebooks or the emails and -- yeah.
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` Q. Okay. So other than the facts that you've laid
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`forth and dating them based on the documents you have
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`that are now part of the binder in front of you --
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` A. (Nods head.)
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` Q. -- are there any other documents that would
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`verify these dates?
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` A. Published papers.
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` Q. Okay.
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` A. Well, yeah. There were also -- besides the
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`notebooks that I kept, I had a lot of data analysis done
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`on hard drives. And those should also have the date,
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`like the file creation date and modification date, that
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`should also support what I have done.
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` Q. Okay. So other than the documents that are in
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`the notebook that we've talked about this morning that
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`you have right in front of you --
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` A. Uh-huh.
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` Q. -- the published papers --
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` A. Uh-huh.
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` Q. -- and the hard drive that contains file
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`creation dates for various data that was generated and
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`stored, are there any other documents that would verify
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`the dates that are contained in your declaration?
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` A. Not that I can recall at the moment.
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` Q. And what other publications do you have in mind
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`besides the PNAS paper that is part of your declaration
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`that would verify the dates in your declaration?
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` A. There was a paper in PLOS ONE that was a
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`follow-up of the PNAS paper that was published a year
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`after and that talked about the GC correction.
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` Q. Did that have additional data relative to the
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`PNAS paper, or was it just, kind of, another version of
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`it published in a different journal?
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` A. It was the same data, but a different or
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`improved analysis method.
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` Q. Okay. I apologize. I may have asked this one,
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`but I just want to make sure I got it right. Other than
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`the documents that are in your exhibit in the notebook in
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`front of you that are referenced in your declaration
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`exhibit, I think it's 2132. Yeah, 2132. That's right on
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`the front page of that -- if you just flip to the front
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`on the very bottom, do you see Exhibit 2132?
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` A. Uh-huh.
`
` Q. Okay. So other than exhibits that are
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`referenced in Exhibit 2132, your declaration, and you
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`have them in front of you in this notebook --
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` A. Yeah.
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` Q. -- the paper you identified for me, the
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`follow-on paper on GC correction --
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` A. Uh-huh.
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` Q. -- and the data that's stored in the hard drives
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`that you mentioned for me about the file creation date,
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`is there any other documentation that would verify the
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`dates that are set forth in your declaration,
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`Exhibit 2132?
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` A. Not that I can recall.
`
` Q. Okay. Thank you.
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` All right. Now, if we push forward to paragraph
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`13, do you want to take a moment to read it? I'm going
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`to ask you questions about paragraph 13.
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` A. I'm done reading it.
`
` Q. Okay. Okay. And if you push to -- you might as
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`well pull out Exhibit 2109, and I believe one of the
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`differences between the corrected 2109, that added
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`additional pages, and the original 2109 --
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` MR. COCKRUM: Do you need a copy of the
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`corrected version?
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` MR. WISE: No. I printed it. Thank you.
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` Q. Is pages 70 and 71; is that correct?
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` A. Was that a question for me?
`
` Q. Let me withdraw it and rephrase it.
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` What are the differences between the corrected
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`notebook exhibit, Number 2109, and the one that was
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`originally submitted?
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` A. I believe there were some missing pages in the
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`original version that didn't have some of the pages for
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`this particular exhibit.
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` Q. Do you know which ones they are -- were -- are?
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` A. There were a couple, but I specifically didn't
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`mark them.
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` Q. Fair enough. Let me ask you a different
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`question. Let me ask you a different question.
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` When you signed your declaration, did you go
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`through and look at all the exhibits that were referenced
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`in it and verify the accuracy?
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` A. I did.
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` Q. Okay. So when you signed your declaration, you
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`were looking at an Exhibit 2109 that had pages 70 and 71
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`in it; right?
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` A. As I recall, I think I did see the missing
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`pages.
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` Q. Okay. And wouldn't you agree with me one of the
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`differences between 2109 corrected versus 2109 submitted
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`is pages 70 and 71 are missing in the one that was
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`submitted versus the one that was corrected?
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` A. I think there were additional pages that were
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`also missing, but --
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` Q. Okay. Which ones do you think -- you know,
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`let's --
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` MR. WISE: Do you mind just telling me what the
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`differences are? I didn't spend a lot of time looking at
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`them.
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` MR. COCKRUM: For 2109, it's pages 70 to 78.
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`And for 2110, pages 18 to 71, 96 to 108 and page 86.
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` MR. WISE: Okay. Counsel, thank you for the
`
`clarification.
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` Q. All right. Let's focus on 70 and 71. How does
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`70 and 71 show conception of the count? And if you need
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`some help with the count, you can go back to paragraph 8
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`of Exhibit 2132 of your declaration.
`
` A. So the experiments on page 70 of the notebook --
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` Q. Uh-huh.
`
` A. -- outline the plasma DNA extraction from
`
`patients 27, 28, 31, 32, 35, 36 and 37, and some of --
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`some of the samples were later converted into sequencing
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`library and sequenced, and they became part of the data
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`that we presented in the PNAS paper, I believe.
`
` Q. Okay.
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` MR. WISE: Mr. Videographer, are you good to go?
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` THE VIDEOGRAPHER: I'm good.
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` MR. WISE: Okay. Thank you. Don't hesitate to
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`interrupt me if you need to create a better record.
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` THE VIDEOGRAPHER: Thank you.
`
` Q. BY MR. WISE: Okay. I'm looking at page 71 --
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`sorry. I apologize. I'm looking at page 70, and then if
`
`I look at 71 -- on page 70, I see on the bottom of the
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`page 70, you know, a chart, a graph -- not a chart --
`
`it's a chart. It's a table. It's a table. I apologize.
`
`It's a table. And it references a dye called "HEX," and
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`when I move over to 71, I see a table that references a
`
`dye called "FAM."
`
` A. Right.
`
` Q. What are they referencing?
`
` A. So this is a TaqMan PCR assay that is a duplex
`
`assay where you have two dyes, FAM and HEX. In this
`
`particular assay that I had, FAM was used for detecting
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`DOIS 14, which is a gene on chromosome Y, and then HEX is
`
`a dye to detect GAPDH, which is a housekeeping gene.
`
` Q. So this doesn't relate to the digital PCR work
`
`you were doing with FAM and HEX?
`
` A. Which specific digital PCR experiments were you
`
`referring to?
`
` Q. Well, you've done a lot of digital PCR
`
`experiments. Some of them are referenced, for example,
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`in the '017 and '018 patent that talk about using FAM and
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`HEX. Some of them are referenced also in your thesis on
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`using FAM and HEX for detecting chromosome 21 and
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`chromosome 12. Are you saying that's not what the use of
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`these references are here?
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` A. So FAM and HEX are dyes -- like generic dyes you
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`can design your assay -- I mean, you can detect the genes
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`that you want and assign the dye to the genes that you
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`want. And so over the course of my thesis, I did several
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`digital -- I designed several digital PCR assays that
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`used either dyes to detect various different genes.
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` Q. Oh, so the dyes are attached to the probes that
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`would light up the particular signal that you're
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`amplifying in a digital PCR experiment?
`
` A. That is correct.
`
` Q. Okay. So you're saying in this experiment you
`
`were doing it for a different purpose --
`
` A. Yes.
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` Q. -- with a different construct?
`
` THE REPORTER: Is there an answer?
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` MR. WISE: She said, "Yes."
`
` THE WITNESS: Yes.
`
` Q. BY MR. WISE: You're supposed to -- she just
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`caught me not catching you not saying yes or no.
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` THE REPORTER: Excuse me. Can we go off the
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`record?
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` THE VIDEOGRAPHER: Going off the record. The
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`time is 10:33 a.m.
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` (Recess.)
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` THE VIDEOGRAPHER: Back on the record. The time
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`is 10:35 a.m.
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` MR. WISE: Madam Court Reporter, would you be so
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`kind as -- you can't look up a prior question and answer.
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`Okay.
`
` I'm going to try and characterize your
`
`testimony. And you can actually -- you can correct me,
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`but when I first asked you about this paragraph, about
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`page 70 and 71, and I said how is this reflecting a
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`conception of the count in paragraph 8? Do you remember
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`that?
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` A. I do remember.
`
` Q. Okay. And you identified for me the samples
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`that you're referring to in paragraph 13 of these
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`patients, and you thought that they were later used in
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`sequencing -- were referenced in the PNAS paper; is that
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`right?
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` A. As far as I can recall.
`
` Q. Right.
`
` A. Yes, but --
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` Q. Is it possible that these samples were being
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`used for digital PCR?
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` A. It might be possible. If they were used for
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`digital PCR, they would also be in my notebooks, yeah.
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` Q. Would it be in the notebooks that you have with
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`us today?
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` A. It will be in the notebooks -- the full
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`notebooks that -- I don't know if it would be photocopied
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`here, but the entire -- in the entire series of my lab
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`notebooks, it would be in there.
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` Q. Okay. Let me see if I can understand your
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`answer.
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` You have a set of notebooks; correct?
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` A. Yes.
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` Q. Let's say they're from 1 to 5. What are they
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`numbered? Are they numbered 1 to 5 or --
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` A. I believe they are numbered, but they're also in
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`chronological order.
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` Q. Yeah. I mean, well -- so for example,
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`Exhibit 2109 is subject 3, and 2110 is subject 4. Which
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`is kind of where I came up with the 1 to 5 number. I
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`just threw a guess. Just look at the front of 2109, and
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`then look at Exhibit 2110, and you'll see they're
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`numbered 3 and 4.
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` A. Yes. So they should be numbered, yes, according
`
`to that subject number there.
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` Q. Okay. So we know there's at least 3 and 4. Do
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`you believe there was a 1 and a 2?
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` A. There were 1, 2 -- 1 and 2.
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