PTO/SB/05 (08-08)
`Approved for use through 09/30/2010. OMB 0651-0032
`U.S. Patent and Trademark Office. U.S. DEPARTMENT OF COMMERCE
`Under the Paperwork Reduction Act of 1995 no persons are required to respond to a collection of information unless it displavs a valid OMB control number.
`
`UTILITY
`PATENT APPLICATION
`TRANSMITTAL
`
`Attorney Docket No.
`
`001107.00866
`
`First Inventor
`
`Title
`
`Bert VOGELSTEiN et ai.
`
`DIGITJ.\L J.\MPLIFICATION
`
`(Only for new nonprovisional applications under 37 CFR 1.53(b))
`
`Express Mail Label No.
`
`APPLICATION ELEMENTS
`See MPEP chapter 600 concerning utility patent application contents.
`
`ADDRESS TO:
`
`Commissioner for Patents
`P.O. Box 1450
`Alexandria VA 22313-1450
`
`""""
`
`.I
`
`r
`
`'
`
`1.0 Fee Transmittal Form (e.g., PTO/SB/17)
`
`ACCOMPANYING APPLICATION PARTS
`
`2.0 Applicant claims small entity status.
`See 37 CFR 1.27.
`[Total Pages
`3.[]] Specification
`30
`Both the claims and abstract must start on a new page
`(For information on the preferred arrangement, see MPEP 608.01(a))
`[Total Sheets
`4.[]] Drawing(s) (35 U.S.C. 113)
`7
`
`5. Oath or Declaration
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`[Total Sheets
`
`2
`
`b.
`
`A copy from a prior application (37 CFR 1.63(d))
`
`a. 53 Newly executed (original or copy)
`0orcontinuationldivisional with Box 18 completed)
`
`i.
`
`DELETION OF INVENTOR(S)
`Signed statement attached deleting inventor(s)
`name in the prior application, see 37 CFR
`1.63(d)(2) and 1.33(b).
`
`6.[Z] Application Data Sheet. See 37 CFR 1. 76
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`7.0 CD-ROM or CD-R in duplicate, large table or
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`a. 0
`b.
`Specification Sequence Listing on:
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`CD-ROM or CD-R (2 copies); or
`Paper
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`1
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`l
`1
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`9. 0
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`Assignment Papers (cover sheet & document(s))
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`Name of Assignee The Johns HoQkins University
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`10. 0
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`37 CFR 3.73(b) Statement
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`OPowerof
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`11.0 English Translation Document (if applicable)
`12. 0 lnfoEjtion Disclosure Statement (PTO/SB/08 or PT0-1449)
`Copies of citations attached
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`15. O Certified Copy of Priority Document(s)
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`16. 0 Nonpublication Request under 35 U.S.C. 122(b)(2)(B)(i).
`Applicant must attach form PTO/SB/35 or equivalent.
`CZJ Other: Please use tile CRF from Qarent 09/~181, 35f3
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`17.
`
`filed on Nov. 14, 2003. Contents are identicaL
`
`0
`i.
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`ii.
`C. 0
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`18. If a CONTINUING APPLICATION, check appropriate box, and supply the requisite information below and in the first sentence of the
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`
`Continuation-in-part (CIP)
`
`of prior application No.: 12/6.17,36.8 .................
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`Prior application information:
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`Examiner Samuei C. WOOLWINE
`
`Art Unit: 1 f337
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`19. CORRESPONDENCE ADDRESS
`
`[{]The address associated with Customer Number: I
`
`22907
`
`I OR D Correspondence address below
`
`Name
`
`Address
`
`City
`
`Country
`
`I State
`1 Telephone
`
`Zip Code
`
`Email
`
`Signature
`
`Name
`_(Print/Type)
`
`/Sarah A Kagani
`
`Sarah A. Kagan
`
`1 Date March 24, 2011
`Registration No. I '"
`;,2, 141
`(Attorney/ Agent)
`
`This collection of information is required by 37 CFR 1.53(b). The information is required to obtain or retain a benefit by the public which is to file (and by the
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`If you need assistance in completing the form, call 1-800-PT0-9199 and select option 2.
`
`MYR 1007
`Myriad Genetics, Inc. et al. (Petitioners) v. The Johns Hopkins University (Patent Owner)
`IPR For USPN 7,824,889
`
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`PTO/SB/14 (11-08)
`Approved for use through 09/30/2010. OMB 0651-0032
`U.S. Patent and Trademark Office; U.S. DEPARTMENT OF COMMERCE
`Under the Paperwork Reduction Act of 1995, no persons are required to respond to a collection of information unless it contains a valid OMB control number.
`
`Application Data Sheet 37 CFR 1.76
`
`Attorney Docket Number
`
`001107.00866
`
`Application Number
`
`Title of Invention
`
`Digital Amplification
`
`The application data sheet is part of the provisional or nonprovisional application for which it is being submitted. The following form contains the
`bibliographic data arranged in a format specified by the United States Patent and Trademark Office as outlined in 37 CFR 1.76.
`This document may be completed electronically and submitted to the Office in electronic format using the Electronic Filing System (EFS) or the
`document may be printed and included in a paper filed application.
`
`Secrecy Order 37 CFR 5.2
`D Portions or all of the application associated with this Application Data Sheet may fall under a Secrecy Order pursuant to
`37 CFR 5.2 (Paper filers only. Applications that fall under Secrecy Order may not be filed electronically.)
`r
`lPPIICan t I f
`A
`n orma 1on:
`f
`Applicant 1
`Applicant Authority (!)Inventor I 0Legal Representative under 35 U.S.C. 117
`Prefix Given Name
`Middle Name
`
`Family Name
`
`Suffix
`
`I Remove I
`I 0Party of Interest under 35 U.S.C. 118
`
`VOGELSTEIN
`Bert
`0 Non US Residency O Active US Military Service
`Residence Information (Select One) (!) US Residency
`I Country of Residence i I US
`Baltimore
`State/Province I MD
`City
`us
`
`Citizenship under 37 CFR 1.41(b) i
`
`Mailing Address of Applicant:
`3700 Breton Way
`Address 1
`
`Address 2
`I Baltimore
`
`City
`
`Postal Code
`
`21208
`
`I State/Province
`I Countryi 1 us
`
`Applicant2
`Applicant Authority (!)Inventor I 0Legal Representative under 35 U.S.C. 117
`Prefix Given Name
`Middle Name
`
`I MD
`
`I Remove I
`I 0Party of Interest under 35 U.S.C. 118
`
`Family Name
`
`Suffix
`
`W.
`Kenneth
`KINZLER
`0 Non US Residency 0 Active US Military Service
`Residence Information (Select One) (!) US Residency
`I Country of Residence i I us
`Baltimore
`State/Province I MD
`City
`us
`
`Citizenship under 37 CFR 1.41(b) i
`
`Mailing Address of Applicant:
`1403 Hal kirk Way
`
`Address 1
`
`Address 2
`I Baltimore
`Postal Code
`
`City
`
`21015
`
`I State/Province
`I Countryi I us
`All Inventors Must Be Listed - Additional Inventor Information blocks may be
`generated within this form by selecting the Add button.
`
`I MD
`
`I
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`For further information see 37 CFR 1.33(a).
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`PTO/SB/14 (11-08)
`Approved for use through 09/30/2010. OMB 0651-0032
`U.S. Patent and Trademark Office; U.S. DEPARTMENT OF COMMERCE
`Under the Paperwork Reduction Act of 1995, no persons are required to respond to a collection of information unless it contains a valid OMB control number.
`
`Application Data Sheet 37 CFR 1.76
`
`Attorney Docket Number
`
`001107.00866
`
`Application Number
`
`Title of Invention
`
`Digital Amplification
`
`Customer Number
`
`22907
`
`Email Address
`
`Application Information:
`
`Title of the Invention
`
`Digital Amplification
`
`Attorney Docket Number 001107.00866
`
`Application Type
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`Nonprovisional
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`Subject Matter
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`Utility
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`Suggested Class (if any)
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`Suggested Technology Center (if any)
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`Add Email
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`Total Number of Drawing Sheets (if any)
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`D Request Early Publication (Fee required at time of Request 37 CFR 1.219)
`Request Not to Publish. I hereby request that the attached application not be published under 35 U.S.
`D C. 122(b) and certify that the invention disclosed in the attached application has not and will not be the subject of
`an application filed in another country, or under a multilateral international agreement, that requires publication at
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`2009-11-12
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`PTO/SB/14 (11-08)
`Approved for use through 09/30/2010. OMB 0651-0032
`U.S. Patent and Trademark Office; U.S. DEPARTMENT OF COMMERCE
`Under the Paperwork Reduction Act of 1995, no persons are required to respond to a collection of information unless it contains a valid OMB control number.
`
`Application Data Sheet 37 CFR 1.76
`
`Attorney Docket Number
`
`001107.00866
`
`Application Number
`
`Title of Invention
`
`Digital Amplification
`
`Application
`Number
`
`Continuity Type
`
`Prior Application
`Number
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`Filing Date
`(YYYY-MM-DD)
`
`Patent Number
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`Issue Date
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`12617368
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`Continuation of
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`11709742
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`2007-02-23
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`Prior Application Status Abandoned
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`Application Number
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`Continuity Type
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`Prior Application Number
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`7824889
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`2010-11-02
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`Filing Date (YYYY-MM-DD)
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`11709742
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`Continuation of
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`10828295
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`10828295
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`Division of
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`09981356
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`2001-10-12
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`Prior Application
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`
`Filing Date
`(YYYY-MM-DD)
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`09981356
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`Continuation of
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`09613826
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`2000-07-11
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`2004-04-21
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`6753147
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`2004-06-22
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`6440706
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`2002-08-27
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`Filing Date (YYYY-MM-DD)
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`non provisional of
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`60146792
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`1999-08-02
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`of the CFR to have an assignment recorded in the Office.
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`~
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`I The Johns Hopkins University
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`PTO/SB/14 (11-08)
`Approved for use through 09/30/2010. OMB 0651-0032
`U.S. Patent and Trademark Office; U.S. DEPARTMENT OF COMMERCE
`Under the Paperwork Reduction Act of 1995, no persons are required to respond to a collection of information unless it contains a valid OMB control number.
`
`Application Data Sheet 37 CFR 1.76
`
`Attorney Docket Number
`
`001107.00866
`
`Application Number
`
`Title of Invention
`
`Digital Amplification
`
`Mailing Address Information:
`
`Address 1
`
`Address 2
`
`City
`
`Country il
`
`Phone Number
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`Email Address
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`3400 N. Charles Street
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`Baltimore
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`State/Province
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`21218
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`Signature
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`/Sarah A. Kagan/
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`Date (YYYY-MM-DD) 2011-03-24
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`First Name
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`Sarah A.
`
`I Last Name I Kagan
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`Registration Number
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`32141
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`This collection of information is required by 37 CFR 1.76. The information is required to obtain or retain a benefit by the public which
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`a patent application or patent. Accordingly, pursuant to the requirements of the Act, please be advised that: (1) the general authority for the collection
`of this information is 35 U.S.C. 2(b)(2); (2) furnishing of the information solicited is voluntary; and (3) the principal purpose for which the information is
`used by the U.S. Patent and Trademark Office is to process and/or examine your submission related to a patent application or patent. If you do not
`furnish the requested information, the U.S. Patent and Trademark Office may not be able to process and/or examine your submission, which may
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`The information provided by you in this form will be subject to the following routine uses:
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`The information on this form will be treated confidentially to the extent allowed under the Freedom of Information Act (5 U.S.C. 552)
`and the Privacy Act (5 U.S.C. 552a). Records from this system of records may be disclosed to the Department of Justice to determine
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`A record from this system of records may be disclosed, as a routine use, in the course of presenting evidence to a court, magistrate, or
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`A record in this system of records may be disclosed, as a routine use, to a contractor of the Agency having need for the information in
`order to perform a contract. Recipients of information shall be required to comply with the requirements of the Privacy Act of 1974, as
`amended, pursuant to 5 U.S.C. 552a(m).
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`A record related to an International Application filed under the Patent Cooperation Treaty in this system of records may be disclosed,
`as a routine use, to the International Bureau of the World Intellectual Property Organization, pursuant to the Patent Cooperation Treaty.
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`A record in this system of records may be disclosed, as a routine use, to another federal agency for purposes of National Security
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`A record from this system of records may be disclosed, as a routine use, to the Administrator, General Services, or his/her designee,
`during an inspection of records conducted by GSA as part of that agency's responsibility to recommend improvements in records
`management practices and programs, under authority of 44 U.S.C. 2904 and 2906. Such disclosure shall be made in accordance with the
`GSA regulations governing inspection of records for this purpose, and any other relevant (i.e., GSA or Commerce) directive. Such
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`A record from this system of records may be disclosed, as a routine use, to the public after either publication of the application pursuan
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`7 - ....
`.,. .. -
`,, '
`
`r c)
`)
`i
`JOINTD:t .... LARATION FOR PATENT APPL .. 2ATION
`
`As the below named inventor, we hereby declare that:
`
`Our residence, post office address and citizenship are as stated below next to our names;
`
`We believe we are the original, first and joint inventors of the subject matter which is claimed and for which a
`patent is sought on the invention entitled DlGIIAL AMPLIFICATION, the specification of which
`0
`is attached hereto.
`•
`was filed on July I I, 2000 as Application Serial Number 09/613,826 and was amended on (if
`applicable).
`was filed under the Patent Cooperation Treaty (PCT) and accorded International Application
`No.
`, filed
`, and amended on
`(if any).
`
`0
`
`We hereby state that we have reviewed and unde~stand the contents of the above identified specification,
`including the claims, as amended by any amendment referred to above.
`
`We hereby acknowledge the duty to disclose information which is material to patentability in accordance with -
`Title 37, Code ofFed~ral Regula.tions, §1.56(a).
`
`Prior Foreign Application(s)
`We hereby claim foreign prioritY benefits under Title 35, United States Code, § 119 of any foreign application(s)
`for patent or inventor's certificate listed below and have also identified below any foreign application(s) for patent or
`i':lventor's certificate having a filing date befqre that of the application on which priority is claimed:
`
`Country
`
`Application No.
`
`Date of Filing
`(day month year)
`
`Date oflssue
`(day month year)
`
`Priority Claimed
`Under 3S U.S.C. §119
`
`Prior United States Provisional Application(s)
`We hereby claim priority benefits under Title 35, United States Code, § 1 19(e)(l) of any U.S. provisional
`application listed below:
`
`U.S. Provisional Application No.
`
`601146,792
`
`Date of Filing
`(day month year)
`02 Augustl999
`
`Priority Claimed
`Under 3S U.S.C. §119(e)(l}
`
`Yes
`
`Prior- United States Application(s)
`.
`We hereby claitn the benefit under Title 35, United States Code,§ 120 of any United States application(s) listed(cid:173)
`below and. insofar as the subject matter of each of the claims of this application is not disclosed in the prior United States
`application in the manner provided by the first paragraph ofTitle 35, United States Code, §I) 2, we acknowledge the duty
`to disclose material information as defined in Title 37, Code of Federal Regulations,§ 1 .56( a) which occurred between
`the filing date of the prior application and the national or PCf international filing date of this application:
`
`Application Serial No.
`
`Date of Filing
`(Day, Month, Year)
`
`Status - Patented,
`Pending, Abandoned
`
`BANNER 0. WITCOFF, Lro.
`
`Attorney Docket No. 0 I 107.00031
`Page 1
`
`Page 8 of 396
`
`

`

`,. ,...,
`,., '
`' ....
`
`1
`
`)
`
`:Power of Attorney
`And we liereby· appoint, boih jointly arid severally, as our at1omeys with fulr power' ofStibstifuticih ·and revocation; t<fprosecute ·
`this application and to transact all business in the Patent and Trademark Office co1mected herewith the following attorneys and agents, their
`registration numbers being listed afler their names:
`
`31 ,8 I 0
`ALTHERR, Robert F.
`I 7,037
`BANNER, Donald W.
`29,888
`BANNER, Mark T.
`BANNER, Pamela I.
`33,644
`18,262
`BECKETT, William W.
`42,338
`BODNER, Jordan
`42,373
`BUROW, Scott A.
`20,095
`CALLAHAN, James V.
`42,402
`CHANG, SteveS
`COHAN, Gregory J.
`40,959
`COOPERMAN, Marc S.
`34,143
`34,57 I
`CURTIN, Joseph P.
`39,504.
`DAWSON, John R.
`39,654
`DEMOOR, Laura J.
`35,805
`EVANS, Thomas L.
`FEDOROCHKO, Gary D. 35,509
`FJSHER, WilliamJ.
`32,133
`GLEMBOCKI, Christopher R.38,800
`HANLON, Brian E.
`40,449
`HEMMENDINGER, Lisa M. 42,653
`HONG, Patricia E.
`34,373
`
`.
`
`HOSCHEIT, Dale H.
`IW ANICKJ, John P.
`JACKSON, Thomas H.
`KAGAN, Sarah A.
`KATZ, Robert S.
`KLEIN. William J.
`KRAUSE, Joseph P.
`LINEK, Ernest V.
`MALONE, Dale A.
`MANNA VA, Ashok K.
`McDERMOTT, Peter D.
`McKEE, Christopher L.
`McKJE, Edward F.
`MEDLOCK, Nina L.
`MEECE, Timothy C.
`MEEKER, Frederic M.
`MILLER, Charles L.
`MITRlUS, Janice V.
`MORENO, Christopher P.
`NELSON, Jon 0.
`NJEGOWSKI, James A.
`
`19,090
`34,628
`29,808
`32,141
`36,402
`43,719
`32,578
`29,822
`32,155
`45,301
`29,41 I
`32,384
`17,335
`29,673
`38,553
`35,282
`43,805
`43,808
`38,566
`24,566
`28,331
`
`PATEL, Binal J.
`PATHAK, A jay S.
`PAYNE, Stephen S.
`PETERSON, Thomas L.
`POTENZA, Joseph M.
`PRA IT, Thomas K.
`RENK, Christopher J.
`RESIS, Robert H.
`RIVARD, Paul M.
`SCHAD, Steve P.
`SHANAHAN, Michael H.
`SHJFLEY, Charles W.
`SKERPON, Joseph M.
`STOCKLEY, D. J.
`VANES, J. Pieter
`WITCOFF, Sheldon W.
`WOLFFE, Franklin D.
`WOLFFE, Susan A.
`WRIGHT, Bradley C.
`
`42,065
`38,266
`35,316
`30,969
`28,175
`37,210
`33,761
`32,168
`43,446
`32,550
`24,438
`28,042
`29,864
`34,257
`37,746
`17,399
`19,724
`33,568
`38,061
`
`All correspondence and telephone communications should be addressed to:
`Banner & Witcoff, Ltd.
`Customer Number: 22907
`1001 G Street, N.W., I lth Floor
`Tel: (202) 508-9100
`Washington, D.C. 20001-4597
`Fax: (202) 508-9299
`
`We hereby declare that all statements made herein of our own knowledge are true and that all statements made on information
`and belief are believed to be true; and further that these statements were made with the knowledge that willful false statements and the
`like so made are punishable by fine or i~·sonrnent, or both, under Section 1001 of Title 18 of the United States Code and that such
`nts may jeopardize I e validity of the application or any patent issuing thereon.
`willful falsest
`I I
`
`First Given Name
`Citizenship United States
`
`11/ )rfoo
`
`Date: _ __:._;_.;._~_:_ _ _ _ _ _ _ _ _
`W
`Kenneth
`Second Given Name
`First Given Name
`Citizenship United States
`
`Residence:_.Jl.ii.IWlll!.ll.l;..n:lll.l..;~w_-=:::::_--------­
`Post Office Address
`3700 Breton Way, Baltimore, Macy)and 2 I 208
`
`.,/..
`
`~u \t~'
`Signature ~- ~
`Full Name of Second Inventor
`Family Name
`
`·Residence BelAir. Maxyland
`Post Office Address
`1403 Halkirk Wa)', BelAir Macyland 21015
`
`.>
`l '
`
`.. ·
`
`BANNER 0. WrrCOFF, LTD.
`
`Attorney Docket No. 01107.00031
`Page2
`
`Page 9 of 396
`
`

`

`PATENT
`
`IN THE UNITED STATES PATENT AND TRADEMARK OFFICE
`
`In re Application of
`
`Bert VOGELSTEIN et al
`
`Continuation Application of
`Serial No. 12/617,368
`
`Filed: Herewith
`
`For: DIGITAL AMPLIFICATION
`
`)
`)
`)
`)
`)
`)
`)
`)
`)
`)
`
`Prior Group Art Unit: 163 7
`
`Prior Examiner: Samuel Woolwine
`
`Confirmation No. TBD
`
`Atty. Dkt. No. 001107.00866
`
`RECOGNITION OF PRACTITIONERS OF RECORD UNDER 37 C.F.R. § 1.32(c)(3)
`
`U.S. Patent and Trademark Office
`Customer Service Window
`Randolph Building
`40 1 Dulany Street
`Alexandria, VA 22314
`
`Sir:
`
`Pursuant to 37 C.F.R. § 1.32(c)(3), please recognize the following patent practitioners, originally
`
`named in the Power of Attorney from an earlier-filed application, as being of record in the above(cid:173)
`
`identified application:
`
`Name
`Sarah A. Kagan
`Dale H. Hoscheit
`Joseph M. Skerpon
`Lisa M. Hemmendinger
`William J. Fisher
`
`Registration No.
`32,141
`19,090
`29,864
`42,653
`32,133
`
`A copy of the Power of Attorney from the earlier-filed application is submitted herewith.
`
`Dated: March 24, 2011
`
`Customer No. 22907
`
`Respectfully submitted,
`BANNER & WITCOFF, LTD.
`
`By:
`
`!SARAH A. KAGAN!
`Sarah A. Kagan
`Registration No. 32,141
`
`Page 10 of 396
`
`

`

`DIGITAL AMPLIFICATION
`
`The U.S. government retains certain rights in this invention by virtue of
`
`its support of the underlying research, supported by grants CA 43460, CA
`
`57345, and CA 62924 from the National Institutes of Health.
`
`The disclosure of all claimed priority applications is expressly
`
`incorporated herein.
`
`TECHNICAL FIELD OF THE INVENTION
`
`This invention is related to diagnostic genetic analyses. In particular it
`
`relates to detection of genetic changes and gene expression.
`
`BACKGROUND OF THE INVENTION
`
`In classical genetics, only mutations of the germ-line were considered
`
`important for understanding disease. With the realization that somatic
`
`mutations are the primary cause of cancer, and may also play a role in aging,
`
`new genetic principles have arisen. These discoveries have provided a wealth
`
`of new opportunities for patient management as well as for basic research into
`
`the pathogenesis of neoplasia. However, many of these opportunities hinge
`
`upon detection of a small number of mutant-containing cells among a large
`
`excess of normal cells. Examples include the detection of neoplastic cells in
`
`urine, stool, and sputum of patients with cancers of the bladder, colorectum,
`
`and lung, respectively. Such detection has been shown in some cases to be
`
`possible at a stage when the primary tumors are still curable and the patients
`
`asymptomatic. Mutant sequences from the DNA of neoplastic cells have also
`
`been found in the blood of cancer patients. The detection of residual disease in
`
`lymph nodes or surgical margins may be useful in predicting which patients
`
`1
`
`Page 11 of 396
`
`

`

`might benefit most from further therapy. From a basic research standpoint,
`
`analysis of the early effects of carcinogens is often dependent on the ability to
`
`detect small populations of mutant cells.
`
`Because of the importance of this issue in so many settings, many
`
`useful techniques have been developed for the detection of mutations. DNA
`
`sequencing is the gold standard for the detection of germ line mutations, but is
`
`useful only when the fraction of mutated alleles is greater than ~20%.
`
`Mutant-specific oligonucleotides can sometimes be used to detect mutations
`
`present in a minor proportion of the cells analyzed, but the signal to noise ratio
`
`distinguishing mutant and wild-type (WT) templates is variable. The use of
`
`mutant-specific primers or the digestion of polymerase chain reaction (PCR)
`
`products with specific restriction endon