REQUEST FOR EX PARTE REEXAMINATION TRANSMITTAL FORM
`
`
`
`
`
`Attorney Docket No.:
`465157US110RX
`Date: January 8, 2016
`
`
`Mail Stop Ex Parte Reexam
`Commissioner for Patents
`Alexandria, VA 22313-1450
`
` This is a request for ex parte reexamination pursuant to 37 CFR 1.510 of patent number 8,318,430
`issued November 27, 2012
`. The request is made by:
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` patent owner.
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` third party requester.
`
` The name and address of the person requesting reexamination is:
`Ariosa Diagnostics, Inc.
`5945 Optical Court
`San Jose, CA 95138
`
`
`
`
`
` Credit card payment is being made online (if electronically filed), or is attached hereto (if paper filed), in the amount
`of $12,000.00 to cover the reexamination fee, 37 CFR 1.20(c)(1);
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` Credit to Deposit Account No. 15-0030
` Any refund should be made by
`37 CFR 1.26(c). If payment is made by credit card, refund must be to credit card account.
`
`
`
` A
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`
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` copy of the patent to be reexamined having a double column format on one side of a separate paper is enclosed.
`37 CFR 1.510(b)(4)
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` CD-ROM or CD-R in duplicate, Computer Program (Appendix) or large table
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` Landscape Table on CD
`
`
`Nucleotide and/or Amino Acid Sequence Submission
`If applicable, items a. – c. are required.
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` Computer readable Form (CRF)
`a.
`b. Specification Sequence Listing on:
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`i.
`ii.
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`c.
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` CD-ROM (2 copies) or CD-R (2 copies); or
` paper
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` Statements verifying identity of above copies
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` A copy of any disclaimer, certificate of correction or reexamination certificate issued in the patent is included.
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` Reexamination of claim(s) 1-30
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`is requested.
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` copy of every patent or printed publication relied upon is submitted herewith including a listing thereof on
`Form PTO/SB/08, PTO-1449, or equivalent.
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`An English language translation of all necessary and pertinent non-English language patents and/or printed
`publications is included.
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` A
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`Page 1 of 2
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`IPR2013-00276
`Ariosa Exhibit 1051, pg. 1
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` The attached detailed request includes at least the following items:
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`a.
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` A
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` statement identifying each substantial new question of patentability based on prior patents and printed
`publications. 37 CFR 1.510(b)(1)
`b. An identification of every claim for which reexamination is requested, and a detailed explanation of the
`pertinency and manner of applying the cited art to every claim for which reexamination is requested.
`37 CFR 1.510(b)(2)
`
` A proposed amendment is included (only where the patent owner is the requester). 37 CFR 1.510(e)
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` a. It is certified that a copy of this request (if filed by other than the patent owner) has been served in its entirely
`on the patent owner as provided in 37 CFR 1.33(c).
`The name and address of the party served and the date of service are:
`
`
`WILSON SONSINI GOODRICH & ROSATI – VERINATA
`650 Page Mill Road
`Palo Alto, CA 94304
`
`Date of Service: January 8, 2016
` b. A duplicate copy is enclosed since service on patent owner was not possible.
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`; or
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`12.
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`13.
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`14.
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`15.
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`Correspondence Address: Direct all communication about the reexamination to:
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` The address associated with Customer Number:
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`22850
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`16.
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`The patent is currently the subject of the following concurrent proceeding(s):
` a. Copending reissue Application No.
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` b. Copending reexamination Control No.
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` c. Copending Interference No.
` d. Copending litigation styled:
`
`Verinata Health, Inc. et al. v. Ariosa Diagnostics, Inc. et al., Case No. 3:12-cv-05501-SI (N.D. Cal),
`currently stayed
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`January 8, 2016
`Date
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`46,045
` Registration No.
`
` For Patent Owner Requester
` For Third Party Requester
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`Page 2 of 2
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`
`
` /Greg H. Gardella/
`Authorized Signature
`
`
`
`Greg H. Gardella
`Typed/Printed Name
`
`
`10/08
`
`IPR2013-00276
`Ariosa Exhibit 1051, pg. 2
`
`

`
`Form PTO 1449
`(Modified)
`
`U.S. DEPARTMENT OF COMMERCE
`PATENT AND TRADEMARK OFFICE
`
`LIST OF REFERENCES CITED BY APPLICANT
`
`
`ATTY DOCKET NO.
`465157US110RX
`APPLICANT
`Yue-Jen CHUU, et al.
`
`FILING DATE
`Herewith
`U.S. PATENT DOCUMENTS
`
`SHEET 1 OF 1
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`CONTROL NO.
`Not yet assigned
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`GROUP
`Not yet assigned
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`A
`B
`C
`D
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`E
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`F
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`G
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`R
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`S
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`EXAMINER
`INITIAL
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`Examiner
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`DATE
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`NAME
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`CLASS
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`DOCUMENT
`NUMBER
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`Chuu et al.
`11/27/12
`8,318,430
`
`Dhallan
`02/19/08
`7,332,277
`
`Dhallan
`06/08/06
`2006/0121452
`
`Shoemaker et al.
`04/17/08
`2008/0090239
`OTHER REFERENCES (Including Author, Title, Date, Pertinent Pages, etc.)
`
`SUB
`CLASS
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`
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`
`
`FILING DATE
`IF APPROPRIATE
`
`
`
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`
`
`Prosecution history of U.S. Patent No. 8,318,430 (U.S. Patent Application No.
`13/368,035)
`The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454
`Parallel Sequencing, Jonas Binladen et al., PLoS ONE. 2007; 2(2): e197 (“Binladen”)
`Identification of Genetic Variants Using Barcoded Multiplexed Sequencing, Nat. Methods, Craig et al., Nat. Methods,
`5(10):887-93 (2008) (“Craig”)
`
`Illumina Brochure “Multiplexed Sequencing with the Illumina Genome Analyzer System”, 2008 (“Illumina Brochure”)
`
`A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing,
`Parameswaran, et al., Nucleic Acids Research, 35(19):e130 (2007) (“Parameswaran”)
`Error-correcting barcoded primers allow hundreds of samples to be pyrosequenced in multiplex, Hamady, et al., Nat.
`Methods, 5(3):235-37 (2008) (“Hamady”)
`
`Decision Denying Institution of Inter Partes Review: IPR2015-00873 – USP 7,879,828 (Apotex v. Wyeth)
`
`File History for Inter Partes Review of claims 1-18 of the ‘430 patent (IPR2013-00276)
`
`File History for Inter Partes Review of claims 19-30 of the ‘430 patent (IPR2013-00277)
`
`Supplementary Material referred to on page 8 of Craig
`
`Declaration of Dr. Steven Rosenberg
`
`Appeal No. 2015-1073: Schott Gemtron Corp. v. SSW Holding Company Inc. -- Corrected Brief for Intervenor – Director of
`the United States Patent and Trademark Office
`Printout of http://www.nature.com/nmeth/journal/v5/n10/full/nmeth.1251.html
`
`Printout of http://www.nature.com/nmeth/journal/v5/n3/full/nmeth.1184.html
`
`Printout of http://nar.oxfordjournals.org/content/35/19/e130.full
`
`Federal Circuit Mandate Entering the Judgment and Order in Case No. 15-1215
`
`Federal Circuit Judgment and Order Vacating the Final Written Decisions in IPR2013-00276 and IPR2013-00277
`
`Claim Chart for the First Ground of Rejection: Dhallan II v. Craig and Illumina Brochure
`
`Claim Chart for the Second Ground of Rejection: Dhallan II v. Parameswaran and Hamady
`
`Claim Chart for the Third Ground of Rejection: Dhallan I v. Binladen
`
`
`
`
`
` Additional References sheet(s) attached
`
`Date considered
`
`
`
`*Examiner: Initial if reference is considered, whether or not citation is in conformance with MPEP 609; Draw line through citation if not in
`conformance and not considered. Include copy of this form with next communication to applicant.
`
`
`IPR2013-00276
`Ariosa Exhibit 1051, pg. 3
`
`

`
`Attorney Docket No.: 465157US
`
`
`
`
`
`
`
`IN THE UNITED STATES PATENT AND TRADEMARK OFFICE
`
`§
`§
`§
`§
`§
`§
`§
`§
`§
`
`REQUEST FOR EX PARTE REEXAMINATION OF
`U.S. PATENT NO. 8,318,430
`
`
`U.S. Patent No. 8,318,430
`
`Issued: November 27, 2012
`
`Filed: Feb. 7, 2012
`
`For: METHODS OF FETAL
`ABNORMALITY DETECTION
`
`Mail Stop Ex Parte Reexam
`Commissioner for Patents
`P.O. Box 1450
`Alexandria, VA 22313-1450
`
`Dear Commissioner:
`
`
`
`Pursuant to the provisions of 35 U.S.C. § 302 and 37 C.F.R. § 1.510 et seq., the
`
`undersigned, on behalf of Ariosa Diagnostics, Inc., requests ex parte patent reexamination of
`
`claims 1-30 of U.S. Patent No. 8,318,430 (“the ‘430 patent,” Exhibit A).
`
`
`
`The ‘430 patent is assigned on its face to Verinata Health, Inc. (“Verinata” or “Patent
`
`Owner”). Formerly known as Artemis Health, Inc., Verinata Health, Inc., is a wholly owned
`
`subsidiary of Illumina, Inc.
`
`Co-Pending Litigation
`
`
`
`The ‘430 patent is the subject of a litigation captioned Verinata Health, Inc. et al. v.
`
`Ariosa Diagnostics, Inc. et al., Case No. 3:12-cv-05501-SI (N.D. Cal), currently stayed.
`
`
`
`Requester notes that USPTO policy dictates that patent reexaminations involved in
`
`concurrent litigation are to be accorded a special status. “Any cases involved in litigation,
`
`whether they are reexamination proceedings or reissue applications, will have priority over all
`
`IPR2013-00276
`Ariosa Exhibit 1051, pg. 4
`
`

`
`Request for Ex Parte Reexamination
`Reexamination of U.S. Patent No. 8,318,430
`
`other cases.” MPEP § 2261. As such, it is respectfully requested that the USPTO accord this
`
`proceeding special status such that it may advance to a timely conclusion.
`
`Ex Parte Patent Reexamination Filing Requirements
`
`
`
`Pursuant to 37 C.F.R. § 1.510(b)(1), statements pointing out at least one substantial new
`
`question of patentability based on material, non-cumulative prior art patents for claims 1-30 of
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`the ‘430 patent are provided in Section VI. of this Request. Although some of these prior art
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`references were previously cited in the record during the original prosecution of the ‘430 patent,
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`these references have not been considered in the new light demonstrated by the proposed
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`substantial new questions of patentability.
`
`
`
`Pursuant to 37 C.F.R. § 1.510(b)(2), reexamination of claims 1-30 of the ‘430 patent is
`
`requested, and a detailed explanation of the pertinency and manner of applying the cited prior art
`
`to claims 1-30 is provided in Section VII. of this Request.
`
`
`
`Pursuant to 37 C.F.R. § 1.510(b)(3), copies of every patent relied upon or referred to in
`
`the statement pointing out each substantial new question of patentability or in the detailed
`
`explanation of the pertinency and manner of applying the cited prior art are provided as Exhibits
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`A-X of this Request.
`
`
`
`Pursuant to 37 C.F.R. § 1.510(b)(4), a copy of the ‘430 patent is provided as Exhibit A of
`
`this Request.
`
`
`
`Pursuant to 37 C.F.R. § 1.510(b)(5), the attached Certificate of Service indicates that a
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`copy of this Request, in its entirety, has been served on Patent Owner at the following address of
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`record for Patent Owner, in accordance with 37 C.F.R. § 1.33(c):
`
`
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`
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`
`
`WSGR/VERINATA
`650 Page Mill Road
`Palo Alto, CA 94304
`
`ii
`
`IPR2013-00276
`Ariosa Exhibit 1051, pg. 5
`
`

`
`Request for Ex Parte Reexamination
`Reexamination of U.S. Patent No. 8,318,430
`
`
`
`Also submitted herewith is the fee set forth in 37 C.F.R. § 1.20(c)(1).
`
`Pursuant to 37 C.F.R. § 1.510(b)(6), Requester hereby certifies that neither the statutory
`
`estoppel provisions of 35 U.S.C. § 315(e)(1) nor 35 U.S.C. § 325(e)(1) prohibit Requester from
`
`filing this ex parte patent reexamination request for two reasons, both of which are explained
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`more detail in Section II., below. First, the Final Written Decision declined to institute trial
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`based on the ground presented herein at Section VII.C on the basis that that ground was
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`redundant with another ground on which trial was instituted. Ex. L at 20; Ex. M at 20-21.
`
`Accordingly, the estoppel provisions of 35 U.S.C. § 315(e)(1) cannot apply to that ground.
`
`Apotex v. Wyeth, IPR2015-00873, Paper 8, p. 9 (“[B]ecause the Board denied institution of [a
`
`ground] as redundant, and Petitioner could not have raised [the ground] again once institution
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`was denied as to that ground. Estoppel under 35 U.S.C. § 315(e)(1), therefore, does not bar
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`Petitioner from maintaining a proceeding before the Office on [that ground]”). Second, estoppel
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`does not apply to the remaining grounds presented herein because on December 23, 2015 the
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`Federal Circuit issued the formal mandate entering the judgment of the Federal Circuit which
`
`vacates the Final Written Decision of the Patent Trial and Appeal Board (PTAB) in the matter of
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`Ariosa Diagnostics, Inc. v. Verinata Health, Inc., IPR2013-00276 and IPR2013-00277. See Exs.
`
`T and U. When a judgment is vacated, the effect is to “nullify the judgment entirely and place
`
`the parties in the position of no trial having taken place at all.” United States v. Williams, 904
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`F.2d 7, 8 (7th Cir. 1990); United States v. Ayres, 76 U.S. 608, 610 (1869) (“[I]t is quite clear, that
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`[an] order granting the new trial has the effect of vacating the former judgment, and to render it
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`null and void, and the parties are left in the same situation as if no trial had ever taken place in
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`the cause.”); see also United States v. Lawson, 736 F.2d 835 (2d Cir.1984) (“It has long been
`
`established … that when a judgment has been reversed and the case remanded for a new trial, the
`
`iii
`
`IPR2013-00276
`Ariosa Exhibit 1051, pg. 6
`
`

`
`Request for Ex Parte Reexamination
`Reexamination of U.S. Patent No. 8,318,430
`
`effect is to nullify the judgment entirely and place the parties in the position of no trial having
`
`taken place”). In a similar context the PTAB held that the one–year bar of 37 C.F.R. § 315(a)
`
`does not apply where a district court complaint was dismissed without prejudice because “[t]he
`
`Federal Circuit has consistently interpreted the effect of such dismissals as leaving the parties as
`
`though the action had never been brought.” Macauto v. BOS GmbH & KG, IPR2012-00004,
`
`Paper 18, p. 15 (PTAB Jan 24, 2013). The same reasoning applies to the estoppel provision of
`
`35 U.S.C. §315(e)(1) – the vacatur of the final written decisions places the parties in the position
`
`as if no final written decisions had been rendered. Ariosa Diagnostics is thus not estopped from
`
`filing the present request under 37 C.F.R. § 315(e)(1) or 37 C.F.R. § 325(e)(1).
`
`
`
`iv
`
`IPR2013-00276
`Ariosa Exhibit 1051, pg. 7
`
`

`
`
`TABLE OF EXHIBITS ................................................................................................................ vii
`I.
`INTRODUCTION .............................................................................................................. 1
`II.
`THE ESTOPPEL PROVISIONS OF 35 USC §§ 315, 325 DO NOT BAR THIS
`REQUEST........................................................................................................................... 5
`CITATION OF PRIOR ART PATENTS AND PRINTED PUBLICATIONS RELIED
`UPON IN REQUEST FOR REEXAMINATION .............................................................. 8
`OVERVIEW OF THE ‘430 PATENT ................................................................................ 9
`A.
`Background of the ‘430 Patent and Level of Skill in the Art ................................. 9
`B.
`Summary of the ‘430 Patent ................................................................................. 10
`C.
`Prosecution History of the ‘430 Patent ................................................................. 11
`The Inter Partes Review Proceedings .................................................................. 12
`D.
`E.
`The Appeal to the Federal Circuit ......................................................................... 15
`CLAIM CONSTRUCTION .............................................................................................. 16
`“selectively enriching a plurality of non-random polynucleotide sequences”
`A.
`(Claims 1 and 19) .................................................................................................. 16
`“at least 100 different non-random polynucleotide sequences selected from a first
`chromosome tested for being aneuploid and at least 100 different non-random
`polynucleotide sequences selected from a reference chromosome” (Claim 1) .... 18
`“at least one chromosome region tested for being aneuploidy” (Claim 19) ......... 19
`“sequence reads corresponding to enriched and indexed fetal and maternal non-
`random polynucleotide sequences” (Claims 1 and 19) ......................................... 19
`“reference chromosome” (Claim 1) or “chromosome control region” (Claim
`19) ......................................................................................................................... 20
`STATEMENT POINTING OUT EACH SUBSTANTIAL NEW QUESTION OF
`PATENTABILITY FOR THE CHALLENGED CLAIMS .............................................. 21
`Subject Matter, Which if Taught by Prior Art Patents or Printed Publications,
`A.
`Raises a Significant New Question of Patentability for the Challenged Claims .. 21
`The Combination of Dhallan II, Craig and the Illumina Brochure Presents a
`Substantial New Question of Patentability for Claims 1-30 of the ‘430 Patent ... 23
`The Combination of Dhallan II, Parameswaran and Hamady Presents a
`Substantial New Question of Patentability for Claims 1-30 of the ‘430 Patent ... 26
`The Combination Dhallan I and Binladen Presents a Substantial New Question of
`Patentability for Claims 1-30 of the ‘430 Patent .................................................. 28
`VII. DETAILED EXPLANATION OF THE PERTINENCE AND MANNER OF
`APPLYING THE PRIOR ART REFERENCES TO EVERY CLAIM FOR WHICH
`REEXAMINATION IS REQUESTED ............................................................................ 31
`
`C.
`D.
`
`B.
`
`E.
`
`B.
`
`C.
`
`D.
`
`III.
`
`IV.
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`V.
`
`VI.
`
`TABLE OF CONTENTS
`
`v
`
`IPR2013-00276
`Ariosa Exhibit 1051, pg. 8
`
`

`
`Request for Ex Parte Reexamination
`Reexamination of U.S. Patent No. 8,318,430
`
`B.
`
`C.
`
`A.
`
`Dhallan II in View of Craig and the Illumina Brochure Renders Obvious Claims
`1-30 of the ‘430 Patent Under (pre-AIA) 35 U.S.C. § 103(a) .............................. 31
`Dhallan II in View of Parameswaran and Hamady Renders Obvious Claims 1-30
`of the ‘430 Patent Under (pre-AIA) 35 U.S.C. § 103(a) ....................................... 64
`Dhallan I in Combination with Binladen Renders Obvious Claims 1-30 of the
`‘430 Patent Under (pre-AIA) 35 U.S.C. § 103(a) ................................................. 97
`VIII. CONCLUSION ............................................................................................................... 127
`
`
`
`vi
`
`IPR2013-00276
`Ariosa Exhibit 1051, pg. 9
`
`

`
`Request for Ex Parte Reexamination
`Reexamination of U.S. Patent No. 8,318,430
`
`Exhibit A
`
`U.S. Patent No. 8,318,430 to Chuu et al. (for reexamination)
`
`TABLE OF EXHIBITS
`
`Exhibit B
`
`
`Exhibit C
`
`Exhibit D
`
`
`Exhibit E
`
`Exhibit F
`
`
`Exhibit G
`
`
`Exhibit H
`
`
`Exhibit I
`
`
`Exhibit J
`
`Exhibit K
`
`Exhibit L
`
`
`Exhibit M
`
`
`Exhibit N
`
`Exhibit O
`
`Exhibit P
`
`
`Exhibit Q
`
`Prosecution history of U.S. Patent No. 8,318,430 (U.S. Patent Application No.
`13/368,035)
`
`U.S. Patent No. 7,332,277 to Dhallan (“Dhallan I”)
`
`The Use of Coded PCR Primers Enables High-Throughput Sequencing of
`Multiple Homolog Amplification Products by 454 Parallel Sequencing, Jonas
`Binladen et al., PLoS ONE. 2007; 2(2): e197 (“Binladen”)
`
`U.S. Patent Pub. App. No. 2006/0121452 to Dhallan II (“Dhallan II”)
`
`Identification of Genetic Variants Using Barcoded Multiplexed Sequencing, Nat.
`Methods, Craig et al., Nat. Methods, 5(10):887-93 (2008) (“Craig”)
`
`Illumina Brochure “Multiplexed Sequencing with the Illumina Genome Analyzer
`System” (2008) (“Illumina Brochure”)
`
`A pyrosequencing-tailored nucleotide barcode design unveils opportunities for
`large-scale sample multiplexing, Parameswaran, et al., Nucleic Acids Research,
`35(19):e130 (2007) (“Parameswaran”)
`
`Error-correcting barcoded primers allow hundreds of samples to
`be pyrosequenced in multiplex, Hamady, et al., Nat. Methods, 5(3):235-37 (2008)
`(“Hamady”)
`
`U.S. Patent Pub. App. No. 2008/0090239 to Shoemaker, et al. (“Shoemaker”)
`
`File History for Inter Partes Review of IPR2015-00873, Paper 8.
`
`File History for Inter Partes Review of claims 1-18 of the ‘430 patent
`(IPR2013-00276)
`
`File History for Inter Partes Review of claims 19-30 of the ‘430 patent
`(IPR2013-00277)
`
`Supplementary Material referred to on page 8 of Craig.
`
`Declaration of Dr. Steven Rosenberg
`
`Solicitor’s brief in Schott Gemtron Corp. v. SSW Holding Co., Appeal No. 2015-
`1073.
`
`Printout of http://www.nature.com/nmeth/journal/v5/n10/full/nmeth.1251.html
`
`vii
`
`IPR2013-00276
`Ariosa Exhibit 1051, pg. 10
`
`

`
`Request for Ex Parte Reexamination
`Reexamination of U.S. Patent No. 8,318,430
`
`Printout of http://www.nature.com/nmeth/journal/v5/n3/full/nmeth.1184.html
`
`Printout of http://nar.oxfordjournals.org/content/35/19/e130.full
`
`Federal Circuit Mandate Entering the Judgment and Order in Case No. 15-1215
`
`Federal Circuit Judgment and Order Vacating the Final Written Decisions in
`IPR2013-00276 and IPR2013-00277
`
`Claim Chart for the First Ground: Dhallan II in combination with Craig and the
`Illumina Brochure
`
`Claim Chart for the Second Ground: Dhallan II in combination with
`Parameswaran and Hamady
`
`Claim Chart for the Third Ground: Dhallan I in combination with Binladen
`
`
`Exhibit R
`
`Exhibit S
`
`Exhibit T
`
`Exhibit U
`
`
`Exhibit V
`
`
`Exhibit W
`
`
`Exhibit X
`
`
`
`viii
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`IPR2013-00276
`Ariosa Exhibit 1051, pg. 11
`
`

`
`I.
`
`INTRODUCTION
`
`This request for reexamination and the proposed grounds of rejection raised herein are
`
`supported by a declaration from Dr. Steven Rosenberg, a pioneer in the diagnostics field that
`
`developed two multivariate diagnostic tests which are in clinical use today. See Ex. O. Dr.
`
`Rosenberg’s declaration summarizes and reflects his knowledge, technical expertise, and
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`understanding of the scope and content of the prior art applied in this request for reexamination.
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`Id. at ¶¶ 2-3, 35-44, MPEP § 2258. The state of the art at the time of the filing of the ‘430 patent
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`is presented by Dr. Rosenberg in this request for reexamination.
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`
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`The ‘430 patent is generally directed to a method for detecting fetal aneuploidies in
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`multiple samples of pregnant women by counting, in a maternal blood sample, the number of
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`DNA fragments from a chromosome suspected of being aneuploid and the number of fragments
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`from a reference chromosome or control region from a chromosome that is not aneuploid. Ex. A
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`at Abstract, 1:23-67, 2:4-11, 6:20-27 and 13:59-64; Ex. O at ¶¶ 14, 45. The two numbers are
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`compared to determine whether there is an abnormal level of DNA associated with the
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`chromosome suspected of being aneuploid. Id.; Id. at ¶¶ 14, 32, 34, and 45. This method is
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`performed in a multiplexed fashion for a plurality of maternal blood samples using indexing (i.e.,
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`tagging or labelling) techniques to distinguish results from different samples. Id. at 22:9-29; Id.
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`at ¶¶ 14, 31, 45 and 48.
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`
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`The USPTO has considered the subject matter claimed in the ‘430 patent allowable
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`because the indexing methods taught in cited secondary references were believed to be
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`incompatible with the sequencing techniques taught in the primary references. See Sections
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`IV.C and IV.D, infra.
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`Neither the ex parte examiner nor the PTAB has addressed the merits of any of the
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`grounds presented in this request, each of which provides a combination of art in which the
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`1
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`IPR2013-00276
`Ariosa Exhibit 1051, pg. 12
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`

`
`Request for Ex Parte Reexamination
`Reexamination of U.S. Patent No. 8,318,430
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`indexing or multiplexing technique is fully compatible with the sequencing method.
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`Parameswaran, P., et al. “A Pyrosequencing-Tailored Nucleotide Barcode Design Unveils
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`Opportunities for Large-Scale Sample Multiplexing.” Nucleic Acids Research, 35(19):e130
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`(2007) (“Parameswaran”) (Ex. H) and Hamady, M., et al. “Error-Correcting Barcoded Primers
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`Allow Hundreds of Samples to be Pyrosequenced in Multiplex.” Nat. Methods, 5(3):235-37
`
`(2008) (“Hamady”) (Ex. I) were not before the PTAB during the inter partes reviews. U.S.
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`Patent Pub. App. No. 2006/0121452 to Dhallan II (“Dhallan II”) was likewise not before the
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`PTAB, although a related Dhallan reference (“Dhallan I”) (U.S. Patent No. 7,332,277, Ex. C)
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`was considered. See, e.g., Ex. L, Paper 11 at 14-20; Ex. M, Paper 11 at 14-21. However, the
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`PTAB expressly declined to consider whether the claimed subject matter was rendered obvious
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`by Dhallan I taken in view of documentation describing commercially available prior art
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`massively parallel sequencing systems. See Ex. L, Paper 43 at 19, Ex. M, Paper 43 at 19.
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`Accordingly, even as to Dhallan I the PTAB did not consider whether that reference rendered the
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`claimed subject matter obvious when considered in combination with then-conventional and
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`commercially available massively parallel sequencing systems.
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`The substantial new questions of patentability presented in this request are
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`straightforward. Dhallan II, filed in 2004, teaches all limitations recited in the claims except the
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`detection method which employs i) indexing or tagging samples from different patients so they
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`can be processed simultaneously (sometimes called multiplexing), and ii) using massively
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`parallel sequencing to sequence the indexed samples. Ex. O at ¶ 35.
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`Neither of these latter techniques was commercially available at the time of the filing of
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`the Dhallan II reference. However, both were present in massively parallel sequencing systems
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`which were commercially available and widely used by scientists by January 23, 2010, the
`
`2
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`IPR2013-00276
`Ariosa Exhibit 1051, pg. 13
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`

`
`Request for Ex Parte Reexamination
`Reexamination of U.S. Patent No. 8,318,430
`
`earliest claimed priority date of the ‘430 patent. See Exs. F and G. For instance, the Illumina
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`Genome Analyzer was available in 2008, as was a Multiplexing Kit which was marketed in
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`conjunction with the Illumina Genome Analyzer. The combined use of the Illumina Genome
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`Analyzer and the Multiplexing Kit were advertised as providing fast, high throughput analysis of
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`multiple samples with high quality data, improved productivity and reduced time and cost. Ex.
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`G at 1. Dr. Rosenberg explains in his declaration that any first year post-doctoral student in a
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`molecular biology laboratory would have considered it routine (and quite advantageous) to
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`perform the techniques utilized in the aneuploidy detection method taught by Dhallan II in 2004
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`using the later-developed Illumina Genome Analyzer and Multiplexing Kit as a replacement for
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`the labor-intensive detection technique actually used in the examples of Dhallan II. Ex. O ¶¶ 62-
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`64; Ex. F (Craig, describing the Illumina Genome Analyzer). The Dhallan II reference expressly
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`envisions that various sequencing methods could be used with the disclosed aneuploidy detection
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`assay, stating “[a]ny method that provides information on the sequence of a nucleic acid can be
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`used,” and lists over 20 different detection methods that could be used in addition to the
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`detection technique actually used in the examples. Ex. E at ¶ [0228]. Thus, the claims of the
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`‘430 patent are rendered obvious by Dhallan II in view of Craig (teaching how to perform
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`multiplexed processing on the Illumina Genome Analyzer) and further in view of the Illumina
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`Multiplexing Kit Brochure. Ex. O at ¶¶ 45-52 and 67-197.
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`The second substantial new question of patentability and proposed rejection is similar.
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`Dhallan II could be alternatively combined with a different massively parallel sequencing
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`platform sold by 454 Life Sciences, later acquired by Roche before the earliest claimed priority
`
`date. The Roche/454 massively parallel sequencing platform also could have been
`
`advantageously used to perform the method disclosed by Dhallan II, as it too is a more efficient
`
`3
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`IPR2013-00276
`Ariosa Exhibit 1051, pg. 14
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`

`
`Request for Ex Parte Reexamination
`Reexamination of U.S. Patent No. 8,318,430
`
`and cost effective detection method than the detection method taught in Dhallan II.
`
`Parameswaran teaches the use of the Roche/454 massively parallel sequencing platform for
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`multiplexed detection of multiple samples (Ex. H), and references such as Hamady teach the
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`efficiency of multiplexing using indexes with the Roche/454 massively parallel sequencing
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`platform (Ex. I). Ex. O at ¶¶ 40-41. Thus the claims of the ‘430 patent also are rendered
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`obvious by Dhallan II in view of Parameswaran (describing large-scale multiplexing using the
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`Roche/454 massively parallel sequencing platform) and further in view of Hamady (describing
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`use of error correcting indexes for multiplexing on the Roche/454 platform). Id. at ¶¶ 53-55,
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`198-326.
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`The third substantial new question of patentability is Dhallan I and Binladen. This
`
`ground was presented in the IPR petitions but the Board chose to institute trial instead on a
`
`related but different ground involving a different primary reference – the combination of
`
`Shoemaker, Dhallan I and Binladen. Ex. L, Paper 11 at 20; Ex. M, Paper 11 at 20. The
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`combination of Dhallan I and B presented herein is fundamentally different that the combination
`
`of Shoemaker, Dhallan I and Binladen addressed during the IPR. The combination of Dhallan I
`
`and Binladen relies on the sequencing techniques of Dhallan I being replaced by those described
`
`in Binladen (i.e., multiplexed massively parallel sequencing). In contrast, the ground considered
`
`in the IPR involved Shoemaker’s sequencing techniques being modified only to include the use
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`of extracellular DNA (from Dhallan I) and multiplexing samples from multiple patients (from
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`Binladen). Ex. L, Paper 1 at 38; Ex. M, Paper 1 at 38. Because the combination of Dhallan I
`
`and Binladen also present the technical teaching believed to be missing from the prior art (a
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`multiplexing method which is compatible with the sequencing method), this combination also
`
`4
`
`IPR2013-00276
`Ariosa Exhibit 1051, pg. 15
`
`

`
`Request for Ex Parte Reexamination
`Reexamination of U.S. Patent No. 8,318,430
`
`presents a substantial new question of patentability and renders the claimed subject matter
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`obvious. Ex. O at ¶¶ 56-61 and 327-466.
`
`II.
`
`THE ESTOPPEL PROVISIONS OF 35 USC §§ 315, 325 DO NOT BAR THIS
`REQUEST
`
`Neither 35 U.S.C. § 315(e)(1) nor 35 U.S.C. § 325(e)(1) prohibit Requester from filing
`
`this ex parte patent reexamination request. Only the former is relevant here, as the latter applies
`
`to Covered Business Method Review proceedings, which have not occurred relative to the ‘430
`
`patent.
`
`Even if the Final Written Decision had not been vacated, the estoppel provision of 35
`
`U.S.C. § 315(e)(1) cannot apply to grounds presented but not included in the trial proceedings.
`
`The Board held in Apotex Inc. v. Wyeth LLC, IPR2015-00873, Paper 8 at 8-9 (Sept. 16, 2015)
`
`(Ex. K) that
`
`An inter partes review does not begin until the Office decides to
`institute review; prior to that point, our Rules refer to a
`‘preliminary proceeding’ that begins with the filing of a petition
`and ends with a decision whether to institute trial. . . . [G]rounds
`raised during the preliminary proceeding, but not made part of the
`instituted trial, are not raised ‘during’ an inter partes review and
`cannot be the basis for estoppel under 35 U.S.C. § 315(e)(1).
`(internal citation omitted).
`
`In Apotex, the Board concluded that the 35 U.S.C. § 315(e)(1) provision did not apply “because
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`the Board denied institution of [a ground] as redundant, and Petitioner could not have raised [the
`
`ground] again once institution was denied as to that ground. Estoppel under 35 U.S.C.
`
`§ 315(e)(1), therefore, does not bar Petitioner from maintaining a proceeding before the Office
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`on [that ground]”. Ex. K at 9. The Director of the United States Patent and Trademark Office
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`likewise has taken the position that § 315(e)(1) estoppel does not apply to grounds on which trial
`
`5
`
`IPR2013-00276
`Ariosa Exhibit 1051, pg. 16
`
`

`
`Request for Ex Parte Reexamination
`Reexamination of U.S. Patent No. 8,318,430
`
`was not instituted. In the solicitor’s brief in Schott Gemtron Corp. v. SSW Holding Co., Appeal
`
`No. 2015-1073, the Office argued that
`
`Contrary to Schott's argument, estoppel does not prevent Schott
`from asserting
`the subset of proposed grounds
`that were
`not part of the IPR proceeding in this case. Under the AIA,
`estoppel applies for "any ground that the petitioner raised or
`reasonably could have raised during that inter partes review."
`
`Ex. P at 38 (emphasis in original, citations omitted).
`
`Here, the Board exercised its discretion and declined to institute on the combination of
`
`Dhallan I and Binladen (presented herein at Section VII.C) on the basis that