throbber
Trials@uspto.gov
`571-272-7822
`
`
`
`
`
`Paper No. 44
`Entered: November 20, 2014
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` 1 RECORD OF ORAL HEARING
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` 2 UNITED STATES PATENT AND TRADEMARK OFFICE
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` 3 - - - - - -
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` 4 BEFORE THE PATENT TRIAL AND APPEAL BOARD
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` 5 - - - - - -
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` 6
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` 7 SEQUENOM, INC.
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` 8 Petitioner
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` 9 v.
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` 10 THE BOARD OF TRUSTEES OF THE LELAND
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` 11 STANFORD JUNIOR UNIVERSITY
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` 12 Patent Owner
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` 13 - - - - - -
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` 14
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` 15 Case IPR2013-00390
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` 16 Patent 8,195,415 B2
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` 17 Oral Hearing Held: Tuesday, August 5, 2014
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` 18
`
`
`
`19 Before: LORA M. GREEN, FRANCISCO C.
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` 20 PRATS, and SCOTT E. KAMHOLZ, Administrative Patent Judges.
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` 21
`
` 22 The above-entitled matter came on for hearing on
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` 23 Tuesday, August 5, 2014, at 2:01 p.m., Hearing Room A, at the
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` 24 U.S. Patent and Trademark Office, 600 Dulany Street,
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` 25 Alexandria, Virginia.
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`
`
` 1
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`

`

`Case IPR2013-00390
`Patent 8,195,415
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`
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` 1 APPEARANCES:
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` 2 ON BEHALF OF THE PETITIONER:
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` 3
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` 4 MICHAEL J. WISE, ESQ.
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` 5 Perkins Coie LLP
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` 6 1888 Century Park East
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` 7 Suite 1700
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` 8 Los Angeles, California 90067-1721
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` 9 310-788-3210
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` 10
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` 11 PATRICK MORRIS, Ph.D., ESQ.
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` 12 Perkins Coie LLP
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` 13 Four Embarcadero Center
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` 14 Suite 2400
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` 15 San Francisco, California 94111-4131
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` 16 415-344-7105
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` 17
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` 18 JOHN PETERSON, ESQ.
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` 19 In-House Counsel
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` 20 Sequenom, Inc.
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` 21 3595 Johns Hopkins Court
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` 22 San Diego, California 92121
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` 23 858-202-9000
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` 24
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` 25
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` 2
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`

`

`Case IPR2013-00390
`Patent 8,195,415
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`
`
` 1 APPEARANCES:
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` 2
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` 3 ON BEHALF OF THE PATENT OWNER:
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` 4
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` 5 R. DANNY HUNTINGTON, ESQ.
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` 6 SETH E. COCKRUM, Ph.D., ESQ.
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` 7 SHARON E. CRANE, Ph.D.
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` 8 Rothwell, Figg, Ernst & Manbeck, P.C.
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` 9 607 14th Street, N.W.
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` 10 Suite 800
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` 11 Washington, D.C. 20005
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` 12 202-783-6040
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` 13
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` 14 MARCUS BURCH, ESQ.
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` 15 Representative for Illumina, Inc.
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` 16 5200 Illumina Way
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` 17 San Diego, California 92122
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` 18
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` 19
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` 20
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` 21
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` 22
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` 23
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` 24
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`

`

`Case IPR2013-00390
`Patent 8,195,415
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`
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` 1 P R O C E E D I N G S
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` 2 (2:01 p.m.)
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` 3 JUDGE GREEN: Good afternoon. Please be seated.
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` 4 Welcome, everybody. This is the final oral hearing for
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` 5 IPR2013-00390, which involves Patent Number 8,195,415.
`
` 6 The Board instituted inter partes review in this
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` 7 proceeding on December 9, 2013.
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` 8 At this time we would like counsel to introduce
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` 9 yourselves and your colleagues, beginning with Petitioner.
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` 10 MR. WISE: Your Honor, my name is Michael Wise. I
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` 11 am lead counsel for Petitioner, Sequenom.
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` 12 With me is my partner, Patrick Morris, and my
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` 13 client, John Peterson, is in-house counsel for Sequenom.
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` 14 JUDGE GREEN: Thank you. Welcome to the Board.
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` 15 Patent Owner?
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` 16 MR. HUNTINGTON: Good afternoon, Your Honors. I
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` 17 am Danny Huntington for the Patent Owner. I have with me at
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` 18 counsel table Dr. Seth Cockrum, who is one of the other
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` 19 attorneys in our office.
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` 20 Behind me is Dr. Sharon Crane, who is backup
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` 21 counsel for this case. And then Mr. Marcus Burch, who is a
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` 22 representative for Illumina, which is a licensee of the
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` 23 Stanford case.
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` 24 JUDGE GREEN: Okay. Thank you very much. Welcome
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` 25 to the Board.
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`
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` 4
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`

`

`Case IPR2013-00390
`Patent 8,195,415
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`
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` 1 Consistent with our trial order, each party has 45
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` 2 minutes to present their argument. Petitioner will proceed
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` 3 first to present its case as to the challenged claims, and
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` 4 you may reserve rebuttal time for the case.
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` 5 Thereafter, Patent Owner will respond, and
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` 6 Petitioner can reserve rebuttal time.
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` 7 Counsel for Petitioner, do you have copies of the
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` 8 demonstratives for the court reporter, opposing counsel and
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` 9 the Panel?
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` 10 MR. WISE: I do.
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` 11 JUDGE GREEN: Thank you.
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` 12 MR. WISE: I have already given one to the court
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` 13 reporter. May I approach the Bench?
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` 14 JUDGE GREEN: Yes, please. And then would you
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` 15 like to reserve any time for rebuttal?
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` 16 MR. WISE: I would, Your Honor. I would like to
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` 17 reserve 10 minutes.
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` 18 JUDGE GREEN: 10 minutes. Okay. Whenever you are
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` 19 ready, you may proceed.
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` 20 MR. WISE: All right. Demonstrative Exhibit 2 is
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` 21 the cover page of the '415 patent. This is the patent
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` 22 involving the IPR that was issued on June 9, 2012. It has a
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` 23 provisional filing date of September 20, 2008.
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` 24 The parties to this proceeding are no strangers to
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` 25 each other. The inventors are Quake and Fan . The Patent
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` 5
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`

`

`Case IPR2013-00390
`Patent 8,195,415
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`
`
` 1 Owner is Stanford. And its licensee is Verinata Health,
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` 2 which is a division of Illumina.
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` 3 The '415 patent is presently being asserted
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` 4 against Sequenom by Stanford and Verinata in a lawsuit
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` 5 pending in the Northern District of California.
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` 6 This '415 patent was also involved in U.S. Patent
`
` 7 Interference Number 105,922. And at that interference party
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` 8 Lo was against party Quake, Quake being this inventive entity
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` 9 here.
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` 10 So it was Stanford versus the Chinese University
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` 11 of Hong Kong. And party Lo assigned its rights to the
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` 12 Chinese University of Hong Kong, and the Chinese University
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` 13 of Hong Kong in turn licensed their rights to Sequenom. That
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` 14 interference is ongoing.
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` 15 There were three other interferences between these
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` 16 parties, parties Quake and Fan and the Lo parties. Those
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` 17 interferences are 105,920, 105,923, and 105,924.
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` 18 Those three interferences broadly involve the
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` 19 subject matter of taking a mixed fetal and maternal DNA
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` 20 sample from a pregnant woman, conducting random massively
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` 21 parallel sequencing on that sample, aligning the sequence
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` 22 reads from the random massive parallel sequencing procedure,
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` 23 and then determining the amounts of a chromosome, such as
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` 24 chromosome 21, versus one or more other chromosomes to detect
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` 25 fetal aneuploidy.
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` 6
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`

`

`Case IPR2013-00390
`Patent 8,195,415
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` 1 At question here today with respect to the '415
`
` 2 patent is whether or not Stanford's claims to using windows
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` 3 with a massively parallel sequencing aneuploidy detection
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` 4 method is patentable.
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` 5 The grounds for patentability that were granted
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` 6 with respect to this IPR are shown on slide 3. There is
`
` 7 really only three that we are going to talk about today based
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` 8 upon the briefing.
`
` 9 The first one is whether or not Lo anticipates
`
` 10 under 102(e) and that would apply to all of t he claims.
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` 11 The second one is ground number 3, which is
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` 12 whether or not the combination of Lo and Wang render claim 13
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` 13 and 16 obvious.
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` 14 And the third one that is in di spute is whether or
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` 15 not claim 17 is obvious over Lo, Wang, Hillier and Smith.
`
` 16 Those are the three issues that are being contested by the
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` 17 parties.
`
` 18 So in terms of the claim construction there is
`
` 19 really one issue. And that was determined by the Board in
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` 20 granting the IPR. Because the terms of the -- because the
`
` 21 claims and the specification define all of the other terms,
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` 22 the only issue is how are windows and sliding window
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` 23 interpreted.
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` 24 This is claim 1. So this -- claim 1, independent
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` 25 claim 1 and independent claim 13 set forth window and sliding
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`
`
` 7
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`

`

`Case IPR2013-00390
`Patent 8,195,415
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` 1 window.
`
` 2 So claim 1 has taking a mixed sample, conducting
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` 3 sequencing, aligning the sequence reads, and then determining
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` 4 values for numbers of sequence tags mapping to chromosome
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` 5 portions by using a number of windows of defined length,
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` 6 within normally and abnormally distributed chromosome
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` 7 portions, to obtain a first value and a second value, and
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` 8 then making a determination of whether or not there is an
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` 9 abnormal distribution.
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` 10 If we look at claim 13, it is similar. Again, you
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` 11 are taking a mixed sample, you are conducting massively
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` 12 parallel sequencing, you are aligning the sequence tags to
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` 13 the reference human genome, and then you are determining
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` 14 numbers of sequence tags mapping to each sliding window.
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` 15 So they are using a sliding window of
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` 16 predetermined length here, and based upon what aligns in that
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` 17 sliding window, do a calculation to determine if there is an
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` 18 abnormal distribution of a chromosome.
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` 19 Slide number 7 just puts these two claim
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` 20 limitations, sliding windows and windows of defined length in
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` 21 front of you, but the claim terms are very cl ear and they
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` 22 have been construed twice by the Board.
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` 23 The first time was with respect to the granting of
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` 24 the inter partes review by this Board. We interpret window
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` 25 in claim 1 to mean a predefined subsection of chromosome of
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` 8
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`

`

`Case IPR2013-00390
`Patent 8,195,415
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` 1 sufficient length to allow a determination of an abnormal
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` 2 chromosome distribution, if present, based on th e number of
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` 3 sequence tags mapping to that chromosomal subsection.
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` 4 Similarly, the Board in the 922 interference, on a
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` 5 substantive motion, had to interpret what windows meant. And
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` 6 again the Board found: Accordingly, on the record before us,
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` 7 Lo's interpretation is reasonable and we construe the term
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` 8 "windows" as a predefined subsection of a chromosome or a
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` 9 chromosome region.
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` 10 In slide 9 we see that the broadest reasonable
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` 11 interpretation of sliding window, as set by this Board in the
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` 12 grant of the request for inter partes review.
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` 13 Accordingly, we interpret sliding window to mean a
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` 14 contiguous, overlapping or nonoverlapping, predefined
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` 15 subsection of a chromosome of sufficient length to allow
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` 16 determination of an abnormal chromosome distribu tion, if
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` 17 present, based on the number of sequence tags mapping to that
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` 18 chromosome subsection.
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` 19 So windows, sliding windows, there are regions of
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` 20 chromosome that are big enough to have sequence tags aligned
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` 21 and then determine whether or not there is an abnormal
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` 22 distribution of a chromosome.
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` 23 In addition, in the papers presented by the Patent
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` 24 Owner, with respect to sliding window, the Patent Owner has
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` 25 now admitted that the term sliding window is the same as a
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` 9
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`

`

`Case IPR2013-00390
`Patent 8,195,415
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`
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` 1 number of windows of predefined length.
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` 2 If you look at the Patent Owner's response at page
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` 3 12 and page 16, and the Detter declaration, Exhibit 2138 at
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` 4 paragraphs 12 through 15, in order to argue that the alleged
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` 5 actual reduction to practice using a sliding window falls
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` 6 within the scope of claim 1, the Patent Owner has argued that
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` 7 sliding window is essentially the same as a window of
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` 8 predefined length, as set forth in claim 1.
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` 9 Now, because the Lo -- is it okay if I refer to
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` 10 our application as Lo II, the published application that is
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` 11 the prior art reference that we are referring to under
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` 12 102(e)? Is that all right?
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` 13 JUDGE GREEN: That's fine.
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` 14 JUDGE PRATS: Lo II, that's how it is referred to
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` 15 in the pleadings.
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` 16 MR. WISE: It is.
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` 17 JUDGE PRATS: I have a question. If we could back
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` 18 up before we move on. There is a lot of case law that says
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` 19 you read the claims in light of the specification.
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` 20 I know the original decision and the decision in
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` 21 the interference were saying, well, we are not going to read
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` 22 things from the specification into the claim, but there is
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` 23 the other side of the coin that Patent Owner is n ow arguing,
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` 24 is that, well, if you really look at the specification of the
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` 25 '415 patent, you really need to read equal into it. That's
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` 10
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`Case IPR2013-00390
`Patent 8,195,415
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` 1 reading it in light.
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` 2 MR. WISE: Understood. So I think if we look at
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` 3 slide 10, this is the decision from the Board in the 922
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` 4 interference.
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` 5 And if you look at this case law, it governs.
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` 6 Basically this case law, Aventis and Liebel -Flarsheim,
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` 7 essentially say, even if every single embodiment requires a
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` 8 specific limitation, if that limitation is not in the claims
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` 9 you cannot read it into the claims.
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` 10 In addition, if Patent Owner really wanted to have
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` 11 a windows of equal length to be the definition of what
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` 12 windows of defined length were, they co uld have written the
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` 13 claim that way. They could have amended the claim in this
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` 14 proceeding, and they didn't do so. So they are stuck with
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` 15 the language they have.
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` 16 In addition, not every single embodiment within
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` 17 their specification uses windows of equal length in the same
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` 18 experiment.
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` 19 JUDGE PRATS: You are referring to, I think,
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` 20 example 8?
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` 21 MR. WISE: I am referring to example 8. So they
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` 22 cannot read into their '415 patent claims a limitation that
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` 23 doesn't exist. They are trying to read their specification
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` 24 into it.
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` 25 And while you look at the specification and
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` 11
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`

`Case IPR2013-00390
`Patent 8,195,415
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` 1 understand the claims in light of the specification, windows
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` 2 of defined length and windows of a predetermined length are
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` 3 not windows of equal length. They would have needed to have
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` 4 defined them that way and they didn't. And there are no
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` 5 words or expressions of manifest exclusion or restr iction
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` 6 with respect to these claim elements.
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` 7 JUDGE PRATS: Their argument back, though, is that
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` 8 the only place that windows of defined length, the actual
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` 9 term in the claim, appears in their column 4 and later on in
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` 10 discussion it talks about using windows of equal length.
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` 11 MR. WISE: I think we are talking about that right
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` 12 here, Your Honor, correct. So their lone reference to equal
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` 13 length with their specification does not establish a clear
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` 14 intention to limit. It is this paragraph.
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` 15 And they argue that this sentence here that says
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` 16 "This is explained in detail below, where a number of windows
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` 17 of defined length are created along a chromosome, the windows
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` 18 being on the order of kilobases in length, whereby a number
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` 19 of sequence tags will fall into many of the windows."
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` 20 And then they get down to here and they say what
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` 21 this means here, where it say "this is explained in detail
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` 22 below," is restricted specifically to this sentence t hat says
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` 23 "By counting sequence tags within a series of predefined
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` 24 windows of equal lengths along different chromosomes, more
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` 25 robust and statistically-significant results may be
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` 12
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`

`Case IPR2013-00390
`Patent 8,195,415
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` 1 obtained."
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` 2 But there is no rationale why, as this is
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` 3 explained below, should not refer to the ensuing 16 pages of
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` 4 specification, including all of the embodiments, and
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` 5 including embodiment 8, that uses two different size windows
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` 6 in one experiment.
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` 7 And notably the last sentence of the paragraph
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` 8 presents equal length windows as optional. In other words,
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` 9 you can get better results if you use equal length windows
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` 10 but it is not a requirement.
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` 11 So let's turn to example 8. Example 8 uses two
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` 12 different size windows in the same experiment. For
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` 13 calculating G/C content and making a G/C bias correction, you
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` 14 use a 20 kilobase nonoverlapping window. To determine
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` 15 whether or not there is an abnormal chromosome distribution,
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` 16 you use a nonoverlapping 50 kilobase window. Two different
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` 17 window lengths in one experiment.
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` 18 And their own inventor, Dr. Fan, confirmed that at
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` 19 deposition. Dr. Fan confirmed that a trisomy detection and
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` 20 G/C bias measurement within the same sample set constitutes a
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` 21 single experiment.
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` 22 Here is the testimony:
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` 23 "Question: Well, there's one sequencing run. Is
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` 24 the data analysis of that part of the experiment?
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` 25 "Answer: It would be part of the experiment.
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` 13
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`Case IPR2013-00390
`Patent 8,195,415
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` 1 "Question: And would that include both the
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` 2 detection or nondetection of trisomy 21 and measuring G/C
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` 3 bias?
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` 4 "Answer: The data would be used for both.
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` 5 "Question: It's part of the same experiment for
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` 6 that group of samples?
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` 7 "Answer: Part of the experiment?
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` 8 "Question: It's the same experiment for that
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` 9 group of samples?
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` 10 "Answer: That group of samples serves as one
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` 11 experiment, yes.
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` 12 "Question: Right.
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` 13 "Answer: Okay.
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` 14 "Question: Start to finish. You know, like if
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` 15 you were publishing a paper just on those samples, you would
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` 16 have your -- it would be one thing. It would be, 'Here's my
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` 17 results. Here's my materials. Here's my procedure."
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` 18 "Answer: What was the question?
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` 19 "Question: It's one experiment with these
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` 20 samples?
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` 21 "Answer: Yes.
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` 22 "Question: Start to finish.
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` 23 "Answer: Uh-huh.
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` 24 "Question: You know, including all the data that
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` 25 you do, all the data analysis, it's all one experiment?
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` 14
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`

`Case IPR2013-00390
`Patent 8,195,415
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` 1 "Answer: I would say that it would be one
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` 2 experiment."
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` 3 The inventor testifies it is one experiment. And
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` 4 their big distinction in their brief is that in every single
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` 5 embodiment, when it is one experiment, it always has one
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` 6 window. And example 8 has two, two different window size
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` 7 lengths.
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` 8 JUDGE KAMHOLZ: In the claim the windows are
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` 9 referred to for determining values for numbers of sequence
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` 10 tags.
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` 11 MR. WISE: Correct.
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` 12 JUDGE KAMHOLZ: How does the size of the G/C
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` 13 window relate to that in example 8?
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` 14 MR. WISE: Hold on. Let me look at the claim
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` 15 language. Well, first of all, G/C content is a dependent
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` 16 claim as well, and it depends off of claim 13, which talks
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` 17 about using a sliding window of predetermined length.
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` 18 JUDGE KAMHOLZ: I was focusing more on claim 1.
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` 19 MR. WISE: Okay. With respect to claim 1,
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` 20 determining values for numbers of sequence tags mapping to
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` 21 chromosome portions by using a number of windows of defined
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` 22 length, you would do the same thing with G/C bias.
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` 23 You are taking the windows and you are dividing
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` 24 them into 20 kilobase windows along the chromosome and
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` 25 measuring the amount of G/C content in the windows and
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` 15
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`

`

`Case IPR2013-00390
`Patent 8,195,415
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` 1 comparing it to another to determine if there is any G/C bias
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` 2 in that sample.
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` 3 JUDGE KAMHOLZ: But the discussion of windows in
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` 4 that limitation of claim 1 concerns sequence tags bias.
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` 5 MR. WISE: Oh, the sequence tags contain the G/C
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` 6 content, right, so it is ATGC, so you are looking at the
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` 7 content of G/C on the sequence tags.
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` 8 So the other argument that Paten t Owner presents
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` 9 as the reason that you always have to have windows of equal
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` 10 length, is because windows are being used for normalization.
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` 11 And, again, this doesn't appear in the claims
`
` 12 themselves, as the Board in the 922 interference noted. The
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` 13 only purpose of windows is to determine the values, first and
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` 14 second values, to determine whether or not there is an
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` 15 abnormal distribution.
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` 16 The claims do not expressly indicate that the
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` 17 windows are used for normalization, and nor do they expressly
`
` 18 indicate that the window must be of equal length. And there
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` 19 is no direction from Fan that windows is a term of art that
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` 20 necessarily requires normalization or windows of equal
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` 21 length.
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` 22 And their own expert testified twice that windows
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` 23 have uses other than normalization. And those uses are
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` 24 mitigation of computational demand of whole genome
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` 25 sequencing, more informative results when you use smaller
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` 16
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`

`

`Case IPR2013-00390
`Patent 8,195,415
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` 1 amounts of information, smaller windows. And Dr. Detter's
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` 2 testimony was noted by the Board in the 922 decision on
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` 3 motions as to why the windows were not limited to windows of
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` 4 equal length because normalization could be used for other
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` 5 things. I'm sorry, the windows could be used for things
`
` 6 other than normalization.
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` 7 So, clearly, the construction of windows to be
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` 8 chromosomal subsections or chromosomal regions is correct,
`
` 9 yet to avoid Lo II as prior art, the Patent Owner argues that
`
` 10 Lo II does not disclose windows, which brings us to the Board
`
` 11 has determined twice that Lo II discloses windows.
`
` 12 The first one is in granting the IPR in paper 7,
`
` 13 finding that, when determining the number of windows, number
`
` 14 of sequence tags mapped to a particular chromosome, one may
`
` 15 count the number of sequence tags mapping to chromosome
`
` 16 regions, that is, subsections of chromosomes, rather than the
`
` 17 entire chromosome.
`
` 18 And in the 922 decision, Lo's interpretation is
`
` 19 reasonable and we construe windows as a predefined subsection
`
` 20 of a chromosome or chromosomal region. And Lo discloses
`
` 21 using chromosome subsections and sets -- chromosome regions
`
` 22 and sets of chromosome regions for detecting an abnormal
`
` 23 distribution of chromosomes, specifically fetal aneuploidy.
`
` 24 So that brings us to their next argument, which is
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` 25 that the windows of Lo II are not defined by size and may
`
`
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` 17
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`

`

`Case IPR2013-00390
`Patent 8,195,415
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` 1 vary. But the '415 patent itself says that window size is
`
` 2 arbitrary. Each window is of sufficient length to contain a
`
` 3 significant number of reads. Sequence tags, having about
`
` 4 20-100 face pairs of sequence. Typically a window will be
`
` 5 between 10 kilobases and 100 kilobases. More typica lly
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` 6 between 40 and 60 kilobases.
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` 7 So the size of the window is arbitrary. And,
`
` 8 therefore, in the '415 patent they are not necessarily
`
` 9 determined or defined by size.
`
` 10 The second argument they make is that the windows
`
` 11 are the tool that are being used to do the testing, not the
`
` 12 thing itself that is being tested.
`
` 13 And in Lo II it explicitly states that a
`
` 14 clinically-relevant chromosomal region can refer to a
`
` 15 polynucleotide sequence corresponding to a segment of a
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` 16 larger genomic sequence, in other words, regions that are
`
` 17 being tested in the region you suspect to have aneuploidy, or
`
` 18 it is the larger genomic sequence itself. And that would be
`
` 19 the portion that is being tested as opposed to the tool.
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` 20 So Lo discloses both the tool and the thing that's
`
` 21 being tested. And, finally, Dr. Gabriel testified that
`
` 22 windows themselves may be testified for aneuploidy. So this
`
` 23 is really a false distinction.
`
` 24 In addition to arguing the Lo II does not disclose
`
` 25 windows, Patent Owner also argues that Lo II does not enable
`
`
`
`

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