/'
`
`0
`
`UTILITY
`PATENT APPLICATION
`TRANSMITTAL
`
`'- (Only for new nonprovisional applications under 37 CFR 1.53(b))
`APPLICATION ELEMENTS
`See MPEP chapter 600 concerning design patent application contents.
`
`1. [8J
`
`2. [8J
`
`3. [8J
`
`GJ
`
`I
`
`Fee Transmittal Form (e.g., PTO/SB/17)
`{Submit an original and a duplicate for fee processing)
`Applicant claims small entity status.
`See 37 CFR 1.27.
`Specification
`[Total Pages
`{preferred arrangement set forth below)
`- Descriptive title of the Invention
`- Cross References to Related Applications
`- Statement Regarding Fed sponsored R & D
`- Reference to sequence listing, a table,
`or a computer program listing appendix
`- Background of the Invention
`- Brief Summary of the Invention
`- Brief Description of the Drawings { if filed)
`- Detailed Description
`-Claim(s)
`- Abstract of the Disclosure
`
`First Inventor
`
`ADDRESS TO
`
`JL IC!l 11,,J! .. ::~i:; .::n .. ::;;;i· [::ll 3::l:
`~ 0 -·
`Attorney Docket No. I 021766-000100US
`I Kordunsky, Igor
`Title I SYSTEMS AND METHODS FOR FLUORESCENCE
`/
`DETECTION WITH A MOVABLE DETECTION MODULE
`I EV 330853907 us
`Express Mail Label No.
`Commissioner for Patents
`Mail Stop Patent Application
`P.O. Box 1450
`Alexandria, VA 22313-1450
`7.0 CD-ROM or CD-R in duplicate, large table or
`Computer Program (Appendix)
`8. Nucleotide and/or Amino Acid Sequence Submission
`(if applicable, all necessary)
`a. 0 Computer Readable Form (CRF)
`b. Specification Sequence Listing on:
`i. 0 CO-ROM or CD-R (2 copies); or
`ii. D paper number of pages
`c. 0 Statements verifying identity of above copies
`ACCOMPANYING APPLICATIONS PARTS
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`Assignment Papers (cover sheet & document(s))
`37 CFR 3.73{b) Statement
`0 Power of
`(when there is an assignee)
`Attorney
`
`11. 0
`
`English Translation Document (if applicable)
`
`12. 0
`
`0 Copies of ID.S
`Citations
`
`[Total Sheets EJ 1
`[Total Pages G:::=J
`
`4. [8J
`Drawing(s) (35 U.S.C.113)
`5. Oath or Declaration
`[8J Newly executed (original or copy)
`a.
`b. 0 Copy from a prior application (37 CFR 1.63 (d))
`(for a continuation/divisional with Box 18 completed)
`i. 0 DELETION OF INVENTOR{S)
`Signed statement attached deleting inventor(s)
`named in the prior application. see 37 CFR
`1.63(d)(2) and 1.33(b).
`6.[8J Application Data Sheet. See 37 CFR 1. 76
`
`J
`
`Information Disclosure
`Statement (IDS)/PT0-1449
`Preliminary Amendment
`13. 0
`14. [8J Return Receipt Postcard (MPEP 503)
`(Should be specifically itemized)
`15.0 Certified Copy of Priority Document(s)
`(if foreign priority is claimed)
`16.0 Nonpublication Request under 35 U.S.C. 122
`(b)(2)(B)(i). Applicant must attach form PTO/SB/35
`or its equivalent
`11. O
`Other:
`18. If a CONTINUING APPLICATION, check appropriate box, and supply the requisite information below and in a preliminary a_mendment,
`or in an Application Data Sheet under 37 CFR 1. 76:
`D Divisional
`D Continuation
`D Continuation-in-part (ClP)
`of prior application No: __ / __
`Examiner - -
`Group Art Unit: __
`Prior application information:
`For CONTINUATION or DIVISIONAL APPS only: The entire disclosure of the prior application, from which an oath or declaration Is supplied
`under Box 5b, Is considered a part of the disclosure of the accompanying continuation or divisional application and Is hereby Incorporated by
`reference. The incorporation can only be relled upon when a portion has been Inadvertently omitted from the submitted application parts.
`19. CORRESPONDENCE ADDRESS
`.----·---- ......... ._ .... _ ....
`·····-·-··· ··--···· -···-
`---······-
`·-···-·····- ····-····
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`181 Customer Number or Bar Code Label
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`20350
`······-·-PATENT TRADEMARK OFFICE ... ··--·-·-·--····-···--· I
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`I
`
`[ _____ ...•
`
`or D Correspondence address below
`
`Name
`
`Address
`
`City
`
`Country
`
`Name (Print/Type),
`
`Signature
`
`I State
`I Telephone
`Cathy E. Cretsinger
`
`IOJ-0 G~clh
`
`I Zip Code
`I Fax
`I Registration No. (Attorney/Agent)
`I Date
`
`51,588
`
`5/8/03
`
`This collection of information is required ~ 37 CFR \~;b). The information is required to obtain or retain a benefit by the public which is to file (and
`by the USPTO to process) an application. Confidenti lily is governed by 35 U.S.C. 122 and 37 CFR 1.14. This collection is estimated to take 12
`minutes to complete, including gathering, preparing, and submitting the completed form to the USPTO. Time will vary depending upon the individual
`case. Any comments n the amount of time you require to complete this form and/or suggestions for reducing this burden, should be sent to the Chief
`Information Officer. U.S. Patent and Trademark Office, U.S. Department of Commerce, P.O. Box 1450, Alexandria, VA 22313-1450. DO NOT SEND
`FEES OR COMPLETED FORMS TO THIS ADDRESS. SEND TO: Commissioner for Patents, Mall Stop Patent Application, P.O. Box 1450,
`Alexandria, VA 22313-1450." SF 1458670 v1 If you need assistance in completing the form, ca/11-800-PT0-9199 and select option 2.
`
`Agilent Exhibit 1204
`Page 1 of 224
`
`

`

`JL CU 1Llk:::~; .::JL ::;;;,- ll]l :!:] m l[:11 ~::ii; H]i :Ei: n1 :::::t
`PTO/SB/17 (05-03)
`Approved for use through 04/30/2003. 0MB 0651-0032
`Patent and Trademark Office: U.S. DEPARTMENT OF COMMERCE
`Under the Paoerwork Reduction Act of 1995 no oersons are reauired ta resoand to a collection af information unless it disolavs a valid 0MB control number.
`Complete II nnown
`
`r
`
`FEE TRANSMITTAL
`for FY 2003
`
`Effective 01/01/2003. Patent fees are subject to annual revision.
`[8] Applicant claims small entity status. See 37 CFR 1.27
`
`Express Mail # EV 330853907 US
`
`METHOD OF PAYMENT (check all that apply)
`
`375
`
`\.._TOTAL AMOUNT OF PAYMENT I ($)
`D Check D Credit Card D MoneyOrder D Other D None
`[8J Deposit Account:
`Deposit
`Account
`Number
`
`120-1430
`
`Deposit
`Account
`Name
`The Commissioner Is authorized to: (check all that apply)
`[8J Charge fee(s) indicated below
`[8J Credit any overpayments
`[8J Charge any additional fee(s) during the pendency or this application
`D Charge fee(s) indicated below, except for the filing fee
`
`I Fee
`f ownsend and Townsend and Crew LLP I
`
`'
`
`Application Number
`
`Not Yet Assigned
`
`Filing Date
`
`May 8, 2003
`
`First Named Inventor
`
`Kordunsky, Igor
`
`Examiner Name
`
`Not Yet Assigned
`
`Art Unit
`
`NYA
`
`Attorney Docket No.
`
`021766-0001 oous
`
`3. ADDITIONAL FEES
`
`FEE CALCULATION (continued)
`
`Large
`
`Code
`1051
`1052
`
`1053
`1812
`1804
`
`Entity
`Fee
`($)
`130
`50
`
`130
`2,520
`920·
`
`Small Entity
`Fee
`Fee
`Code
`($)
`2051
`65
`2052
`25
`
`1053
`1812
`1804
`
`130
`
`920*
`
`Fee Description
`
`Fee
`~
`
`Surcharge - late provisional filing fee
`or cover sheet.
`Non-English specification
`
`Requesting publication of SIR prior to
`Examiner action
`1,840· Requesting publication of SIR after
`Examiner action
`Extension for reply within first month
`Extension for reply within second
`month
`Extension for i:eply within third month
`Extension for reply within fourth
`month
`Extension for reply within fifth month
`Notice of Appeal
`Filing a brief in support of an appeal
`Request for oral hearing
`Petition to institute a public use
`proceeding
`
`55
`205
`
`465
`725
`
`985
`160
`160
`140
`
`1,510
`
`2452
`2453
`2501
`2502
`2503
`1460
`1807
`
`55
`650
`650
`235
`315
`130
`50
`
`1805
`
`1,840*
`
`1805
`
`1251
`1252
`
`1253
`1254
`
`1255
`1401
`1402
`1403
`
`110
`410
`
`930
`1,450
`
`1,970
`320
`320
`280
`
`2251
`2252
`
`2253
`2254
`
`2255
`2401
`2402
`2403
`
`1451
`
`1,510
`
`1451
`
`o the above-identified deposit account.
`FEE CALCULATION
`1. BASIC FILING FEE
`_arge Entity
`Small Entity
`i=ee
`Fee
`Fee
`Fee
`Code
`Code
`($)
`($)
`1001
`750
`375
`2001
`1002 330
`165
`2002
`1003 520
`2003
`260
`1004 750
`375
`2004
`1005 160
`2005
`80
`
`Fee Description
`
`Fee Paid
`
`Utility filing fee §
`
`Design filing fee
`Plant filing fee
`Reissue filing fee
`Provisional filing fee
`
`SUBTOTAL (1)
`
`M$}375
`
`I
`
`2. EXTRA CLAIM FEES FOR UTILITY AND REISSUE
`
`Extra Claims
`
`Fees from
`below
`
`Fee Paid
`
`Surcharge - late filing fee or oath --
`--
`--
`2,520 For filing a request for reexamination --
`--
`---
`--
`--
`----
`---
`--
`---
`--
`--
`---
`Petition to revive - unavoidable --
`----
`---
`--
`---
`- - -
`-
`-
`
`180
`
`40
`
`~
`
`1452
`1453
`1501
`1502
`1503
`1460
`1807
`
`110
`1.300
`1,300
`470
`630
`130
`50
`
`1806
`
`180
`
`1806
`
`8021
`
`40
`
`8021
`
`Petition to revive - unintentional
`Utility issue fee (or reissue)
`Design issue fee
`Plant issue fee
`Petitions to the Commissioner
`Petitions related to provisional
`applications
`Submission of Information Disclosure
`Stmt
`Recording each patent assignment
`per property (times number of
`properties)
`Filing a submission after final rejection
`(37 CFR § 1.129(a))
`For each additional invention to be
`
`Request for Continued Examination
`(RCE)
`Request for expedited examination
`of a design application
`
`-
`examined (37 CFR § 1.129(b)) --
`---
`---
`---
`
`1809
`
`750
`
`2809
`
`375
`
`1810
`
`750
`
`2810
`
`375
`
`1801
`
`750
`
`2801
`
`375
`
`1802
`
`900
`
`1802
`
`900
`
`Other fee (specify)
`
`Total Claims
`
`Independent
`Claims
`
`Multiple
`Dependent
`
`Large Entity
`Fee
`Fee
`Code
`($)
`1202
`18
`1201
`84
`1203
`280
`
`EJ-20-= e
`D -3 * * = E
`
`~mall Entity
`Fee
`Fee
`Code
`($)
`9
`2202
`2201
`42
`140
`2203
`
`1204
`
`84
`
`2204
`
`42
`
`1205
`
`18
`
`2205
`
`9
`
`p#9
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`rE42
`
`~
`
`r Eo
`r E
`r I
`
`I
`
`I
`I
`
`Fee Description
`
`Claims in excess of 20
`Independent claims in excess of 3
`Multiple dependent claim, if not paid
`•• Reissue independent claims
`over original patent
`•• Reissue claims in excess of 20
`and over original patent
`
`SUBTOTAL (2)
`~$)0
`-or number previously paid, if greater, For Reissues, see above
`
`I
`
`*Reduced by Basic Filing Fee Paid SUBTOTAL (3}
`
`($)
`
`I
`
`SUBMITTED BY
`
`Name (Print/Type)
`
`1 E. Cretsinger
`Cathy
`
`Signature
`
`...
`
`I Registration No. (Attorney/Agent) I 51.588
`G»Y-, ~adv-
`Date
`WARNING: irilormatlon _gn this form may become public. Credit card Information should not be
`Included on this form. Provide credit card Information and authorization on PT0-2038.
`This collection of information is required by 37 CFR 1.17 and 1.27. The information is required to obtain or retain a benefit by the public which is to file (and by the
`USPTO to process) an application. Confidentiality is governed by 35 U.S.C. 122 and 37 CFR 1.14. This collection is estimated to take 12 minutes to complete,
`Including gathering, preparing, and submitting the completed application form to the USPTO. Time will vary depending upon the Individual case. Any comments on
`the amount of time you require to complete this form and/or suggestions for reducing this burden, should be sent to the Chief Information Officer, U.S. Patent and
`Trademark Office, U.S. Department of Commerce, P.O. Box 1450, Alexandria, VA 22313-1450. DO NOT SEND FEES OR COMPLETED FORMS TO THIS
`ADDRESS. SEND TO: Commissioner for Patents, P.O. Box 1450, Alexandria, VA 22313-1450. SF 1458672 v1
`If you need assistance in completing the form, call 1-800-PT0-9199 (1-800-786-9199) qnd select option 2.
`
`Comolete (if aoolicablel
`
`Telephone
`
`415-576-0200
`
`5/8/03
`
`I
`
`~
`
`~
`
`Agilent Exhibit 1204
`Page 2 of 224
`
`

`

`City Country |
`
`(Should be specifically itemized)
`4 (for8 continuation/sivisional with Box 18 comfeted)
`Certified Copy of Priority Document(s)
`Pp
`{if foreign priority is claimed)
`i. ] DELETION OF INVENTOR(S
`Nonpublication Request under 35 U.S.C. 122
`Signed statementattached deleting inventor(s)
`(b)(2)(B)(i). Applicant mustattach form PTO/SB/35
`T0300)Ohadee see 37 CFR
`or its equivalent
`~sOther.
`Cl
`6. Application Data Sheet. See 37 CFR 1.76
`18. tf a CONTINUING APPLICATION, check appropriate box, and supply the requisite information below and in a preliminary amendment,
`orin an Application Data Sheet under 37 CFR 1.76:
`.
`of prior application No:
`O Continuation
`O1 Divisional
`Dd Continuation-in-part (CIP)
`Group Art Unit:
`Prior application information:
`Examiner
`For CONTINUATION or DIVISIONAL APPS only: The entire disclosure of the prior application, from which an oath or declaration Is supplied
`under Gox 5h, Is considered a part of the disclosure of the accompanying continuation or divisional application and is hereby incorporated by
`reference. The incorporation can onty be relied upon when a portion has been inadvertently omitted from the submitted application parts.
`19. CORRESPONDENCE ADDRESS
`
`i
`
`:
`SUE
`Mt
`|
`&) Customer Number or Bar Code Label
`20350
`i
`Fonesnnedanureennnnmtnnatc tarsi tenneeeotpn neon entud
`PATENT TRADEMARK OFFICE
`
`Name
`
`
`: Mt All -
`
`/
`
`or
`
`[L)_
`
`Carrespondence address below
`
`-
`
`Address
`
`
`Telephone
`
`Name (Print/Type) .
`
`Registration No. (Attorney/Agent)
`Cathy E. Cretsinger
`
`
`51,588
`
`Signature[Date|5/8/03
`This collection of information is required th
`- yA(b). The infarmation is required to obtain or retain a benefit by the public which is to file (and
`by the USPTO to process) an applicatian. Confidenti¥lity is governed by 35 U.S.C. 122 and 37 CFR 1.14. This collection is estimated ta take 12
`minutes to complete, including gathering, preparing, and submitting the compieted form to the USPTO. Time will vary depending upon the individual
`case. Any comments n the amountof time you require to complete this form and/or suggestions for reducing this burden, should be sent{o the Chief
`Information Officer, U.S. Patent and Trademark Office, U.S. Department of Commerce, P.O. Box 1450, Alexandria, VA 22313-1450. DO NOT SEND
`FEES OR COMPLETED FORMS TO THIS ADDRESS. SEND TO: Commissioner for Patents, Mail Stop Patent Application, P.O. Box 1450,
`Alexandria, VA 22313-1450. SF 1458670 v1/fyou need assistance in completing the form, call 1-800-PTO-9199 and select option 2.
`
`
`
`Agilent Exhibit 1204
`Page 3 of 224
`
`Attorney Docket No.
`
`021766-000100US
`Kordunsky, Igor
`
`SYSTEMS AND METHODS FOR FLUORESCENCE
`DETECTION WITH A MOVABLE DETECTION MODULE
`Express Mail Label No.
`EV 330853907 US
`ADDRESS TO
`Mal'StopPatentAppleation
`P.O. Box 1450
`Alexandria, VA 22343-1450
`7-L] CD-ROM or CD-R in duplicate, large table or
`Computer Program (Appendix)
`8. Nucleotide and/or Amino Acid Sequence Submission
`(if applicable, all necessary)
`a. CJ Computer Readable Form (CRF)
`b. Specification Sequence Listing on:
`i. (1 CD-ROMor CD-R(2 copies); or
`iO paper numberof pages
`‘
`~
`:
`c. [-] Statements veri
`
`)
`
`MAE
`
`05/08/03
`
`Assignment Papers (cover sheet & document(s))
`37 CFR 3.73(b) Statement
`LJ Powerof
`(when there is an assignee)
`Attorney
`English Translation Document(if applicable)
`
`Information Disclosure
`Statement ((DS)/PTO-1449
`Preliminary Amendment
`Return Receipt Postcard (MPEP 503)
`
`C1 Copies of IDS
`Citations
`
`9.
`O
`0.
`10.0
`
`-O
`
`.O
`
`.O
`EI
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`Oo
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`]
`J
`
`UTI LITY
`PATENT APPLICATION
`TRANSMITTAL
`
`(Only for new nonprovisiona!l applications under 37 CFR 1.53(b))
`APPLICATION ELEMENTS
`See MPEP chapter G00 concerning design patent application contenis.
`
`Fee Transmittal Form (e.g., PTO/SB/17)
`(Submit an original and a duplicate for fee processing)
`Applicant claims smail entity status.
`See 37 CFR1.27.
`Pa
`[Total Pages
`Specification
`(preferred arrangementsetforth befaw)
`- Descriptivetitle of the invention
`- Cross References to Related Applications
`- Statement Regarding Fed spansored R & D
`- Reference to sequence listing,a table,
`or a computer program listing appendix
`~ Background of the Invention
`- Bhef Summary of the invention
`- Brief Description of the Drawings( ff filed)
`- Detailed Description
`- Claim(s)
`- Abstract of the Disclosure
`
`£“
`
`s'nbOL9
`
`Old
`
`Mt,
`i
`
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`
`[Total Sheets[7__|
`Drawing(s) (35 U.S.C. 173)
`4. kX
`[Total Pages
`. Oath or Deciaration
`a Newly executed (original or copy)
`b.
`Copy
`fro
`ior application (37 CFR 1.63 (d
`
`Agilent Exhibit 1204
`Page 3 of 224
`
`

`

` Approved for use through 04/30/2003. OMB 0651-0032
`
`
`
`1805
`
`1806
`8021
`
`2809
`
`
`
`2801
`
`1802
`
`180
`40
`
`«375
`
`
`
`375
`
`900
`
`
`
`
`
`
`
`
`f
`u—_
`
`x
`
`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 displays a valid OMB contral number.
`
`
`
`FEE TRANSMITTAL
`Application Number
`Not Yet Assigned
`
`
`for FY 2003
`
`
`May 8, 2003 Fiting Date
`
`Effective 01/01/2003. Patent fees are subject to annual revision.
`First Named Inventor Kordunsky, Igor
`
`Applicant claims small entity status. See 37 CFR 1.27 Not Yet Assigned
`
`
`
` Examiner Name
`
`
`
` Express Mail # EV 330853907 US
`Art Unit
`NYA
`TOTAL AMOUNT OF PAYMENT |
`(3)
`375
`021766-000100US
`
`Attorney Docket No.
`
`
`
`
`FEE CALCULATION(continued
`METHOD OF PAYMENT(check aif that apply)
`
`3. ADDITIONAL FEES
`[C3 Credit Card LJ MoneyOrder Lj Other L] Nene
`LE Check
`
`
`
` Largo
`Enti
`
`
`& Deposit Account:
`
`
`Aesount
`20-1430
`Code
`($)
`Fee Description
`Paid
`
`
`
`
`
`
`~
`2051
`+65
`Surcharge- iate filing fee or oath
`Number
`
`2052
`25
`Surcharge- late provisionalfiling fee
`or cover sheet.
`
`
` Deposit
`
`Account
`1053.
`130
`Nor-English specification
`
`Name
`1812
`2,520‘
`Forfiling a request for reexamination
`
`
`
`1804
`920"
`Requesting publication of SIR prior to
`he Commissioneris authorized ta:
`(check afl that apply)
`
`Examineraction
`
`
`
`el Charge fee(s) indicated below xX Credit any overpayments
`1,840* Requesting publication of SIR after
`
`
`
`Examineraction
`ed Charge any additional fee(s) during the pendencyof this application
`
`
`
`Extension for reply within first month
`55
`2251
`CI Charge fee(s) indicated below, exceptforthefiling fee
`
`
`fo the above-identified deposit account.
`
`
`2252. 205—_Extension for reply within secand
`month
`
`FEE CALCULATION
`
`Extensionfor reply within third month
`
`
`1. BASIC FILING FEE
`Extension for reply within fourth
`2254
`«725
`
`
`month
`Large Entity
`mall Entity
`985
`2255
`Fee Description
`Extension for reply within fifth month
`Fee
`Feo
`Fee
`Fee
`
`
`ode ($} ode=(8) Fae Paid 2401 160 Notice of Appeal
`
`
`
`
`
`
`
`1001
`750
`2001
`375
`Utility filing fee
`75
`2402
`160
`Filing a brief in support of an appeal
`
`
`1002
`330
`002
`165
`Design filing fee
`2403
`140
`Request for oral hearing
`
`
`1451
`1.510
`Petition toinstitute a public use
`1003
`520
`003
`260
`—~Plantfiling fee
`
`
`'
`proceeding
`4004
`750
`2004
`375
`Reissuefiling fee
`Petition to revive — unavoidable
`1005
`160
`‘005
`80
`Provisionalfiling fee
`
`Petition to revive — unintentional
`(375
`SUBTOTAL(1}
`2501
`650
`Utility issue fee (or reissue)
`
`
`2502
`235
`Design issue fee
`2. EXTRA CLAIM FEES FORUTILITY AND REISSUE
`2503
`(315
`Piant issue fee
`
`
`es
`”
`Fees from
`
`
`
`
`
`
`
`Extra Claims 1460=130below Fee Paid Petitions to the Commissioner
`a
`-
`i
`.
`1807
`50
`Petitions related to provisional
`
`
`so
`Total Claims
`20
`-20"
`=
`9
`=
`applications
`
`
`
`
`Independent
`Submission of information Disclosure
`aims
`3 =
`42
`r
`Stmt
`
`
`.
`Recording each patent assignment
`
`
`Null
`_
`per property (times numberof
`
`
`Pp
`,
`properties)
`
`
`mall Entity
`Large Entity
`Filing a submissionafterfinal rejection
`
`
`Fee
`Fee
`Fee
`Fee
`(37 CFR § 1.129{a))
`
`
`p
`a
`A
`.
`
`ode=($) Code {3} Fee Description 2810 375 For each additionalinvention to be
`
`
`
`
`
`Claimsin excess of 20
`examined (37 CFR § 1.128(b))
`1202
`148
`2202
`9
`
`
`
`
`41201
`84
`2201
`42
`independentclaimsin excess of 3
`Request for Continued Examination
`203280
`2203140
`Multiple dependentclaim,if not paid
`(RCE)
`/
`
`** Reissue independent claims
`Requestfor expedited examination
`1204
`84
`2204
`42
`overoriginal patent
`of a design application
`
`1205
`13
`2205
`9
`** Reissue claims in excess of 20
`Other fee (specify) --------------__-
`and overorigina! patent
`“Reduced by Basic Filing Fee Paid
`SUBTOTAL(3)
`
`
`
`Complete(if applicable)
`
`sueTorAt (2)
`“or numberpreviously paid, if greater, For Reissues, see above
`
`SUBMITTED BY
`
`“oesyEQdy “a
`
`Name (Print/Type)
`
`Cathy E. Cretsinger
`
`Registration No. (Attomey/Agent)
`
`Telephone
`
`415-576-0200
`
`information gn this form may becomepublic. Credit card information should not be
`WARNING:
`included onthis form. Provide credit card information and authorization on PTQ-2038.
`This collection of information is required by 37 CFR 1.77 and 1.27. The information is required to obtain or retain a benefit by the public whichis ta file (and by the
`USPTOto process) an application. Confidentiality is govermed by 35 U.S.C. 122 and 37 CFR 1.14. This collection is estimated to take 12 minutes to complete,
`Including gathering, preparing, and submitting the completed application form to the USPTO. Timewill vary depending upon the individual case. Any comments on
`the amount of time you require to camplete this form and/or suggestions for reducing this burden, should be sent to the Chief information Officer, U.S. Patent and
`Trademark Office, U.S. Department of Commerce, P.O. Box 1450, Alexandria, VA 22313-1450. DO NOT SEND FEES OR COMPLETED FORMSTO THIS
`ADDRESS. SEND TO: Commissionerfor Patents, P.O. Box 1450, Alexandria, VA 22313-1450, SF 1458672 v1
`Wfyou nead assistance in completing the form, calf 1-800-PTO-9199 (1-800-786-9199) qnd select option 2.
`
`
`
`Agilent Exhibit 1204
`Page 4 of 224
`
`Agilent Exhibit 1204
`Page 4 of 224
`
`

`

`Application Data Sheet
`
`Application Information
`
`Application number::
`
`Filing Date::
`
`Application Type::
`
`Subject Matter::
`
`Suggested classification::
`
`Suggested Group Art Unit::
`
`CD-ROM or CD-R??::
`
`Number of CD disks::
`
`Number of copies of CDs::
`
`Sequence Submission::
`
`Computer Readable Form (CRF)?::
`
`Number of copies of CRF::
`
`Title::
`
`Attorney Docket Number::
`
`Request for Early Publication::
`Request for Non-Publication::
`
`Suggested Drawing Figure::
`
`Total Drawing Sheets::
`
`Small Entity?::
`Variety denomination name::
`
`Petition included?::
`
`Petition Type::
`
`Not Yet Assigned
`
`05/08/03
`
`Regular
`
`Utility
`
`SYSTEMS AND METHODS FOR
`
`FLUORESCENCE DETECTION WITH A
`
`MOVABLE DETECTION MODULE
`021766-0001 oous
`No
`No
`
`7
`
`Yes
`
`No
`
`Licensed US Govt. Agency::
`
`Contract or Grant Numbers One::
`
`Secrecy Order in Parent Appl.::
`
`No
`
`Page 1
`
`Initial 5/8/03
`
`Agilent Exhibit 1204
`Page 5 of 224
`
`

`

`Applicant Information
`
`Applicant Authority Type::
`
`Primary Citizenship Country::
`
`Status::
`
`Given Name::
`
`Middle Name::
`Family Name::
`
`Name Suffix::
`
`Inventor
`us
`Full Capacity
`
`Igor
`
`Kordunsky
`
`City of Residence::
`
`Newton
`
`State or Province of Residence::
`
`MA
`
`Country of Residence::
`Street of Mailing Address::
`
`US
`19 Payne Road
`
`Newton
`City of Mailing Address::
`State or Province of mailing address:: MA
`
`Country of mailing address::
`Postal or Zip Code of mailing address:: 02461
`
`Page2
`
`Initial 5/8/03
`
`Agilent Exhibit 1204
`Page 6 of 224
`
`

`

`Applicant Authority Type::
`
`Primary Citizenship Country::
`
`Status::
`
`Given Name::
`
`Middle Name::
`
`Family Name::
`
`Name Suffix::
`
`Inventor
`us
`Full Capacity
`
`Jeffrey
`
`A.
`
`Goldman
`
`City of Residence::
`
`State or Province of Residence::
`
`Acton
`
`MA
`
`Country of Residence::
`
`Street of Mailing Address::
`
`US
`24 Washington Drive
`
`City of Mailing Address::
`
`Acton
`
`State or Province of mailing address:: MA
`
`Country of mailing address::
`
`Postal or Zip Code of mailing address:: 01720
`
`Page 3
`
`Initial 5/8/03
`
`Agilent Exhibit 1204
`Page 7 of 224
`
`

`

`Applicant Authority Type::
`
`Primary Citizenship Country::
`Status::
`
`Given Name::
`
`Middle Name::
`
`Family Name::
`
`Name Suffix::
`City of Residence::
`
`Inventor
`
`US
`Full Capacity
`
`Michael
`
`J.
`
`Finney
`
`San Francisco
`
`State or Province of Residence::
`
`CA
`
`Country of Residence::
`Street of Mailing Address::
`
`US
`489 Douglass Street
`
`City of Mailing Address::
`
`San Francisco
`
`State or Province of mailing address:: CA
`
`Country of mailing address::
`
`Postal or Zip Code of mailing address:: 94114
`
`Page4
`
`Initial 5/8/03
`
`Agilent Exhibit 1204
`Page 8 of 224
`
`

`

`Correspondence Information
`Correspondence Customer Number::
`
`20350
`
`Representative Information
`
`Representative Designation::
`
`Representative Number::
`
`Representative Name::
`
`Primary
`Associate
`
`35,933
`51,588
`
`Kevin T. LeMond
`Cathy E. Cretsinger
`
`Domestic Priority Information
`
`Application::
`
`Continuity Type::
`
`Parent Application:: Parent Filing Date::
`
`Foreign Priority Information
`
`Country::
`
`Application number::
`
`Filing Date::
`
`Assignee Information
`
`Assignee Name::
`
`Street of mailing address::
`
`City of mailing address::
`State or Province of mailing address::
`
`Country of mailing address::
`Postal or Zip Code of mailing address::
`
`Page 5
`
`Initial 5/8/03
`
`Agilent Exhibit 1204
`Page 9 of 224
`
`

`

`Attorney Docket No.: 021766-000lOOUS
`
`PATENT APPLICATION
`
`SYSTEMS AND METHODS FOR FLUORESCENCE DETECTION
`
`WITH A MOVABLE DETECTION MODULE
`
`Inventor(s):
`
`Igor Kordunsky
`19 Payne Road
`Newton, MA 02461-1816
`Citizenship: U.S.A.
`
`Jeffrey A. Goldman
`24 Washington Drive
`Acton, MA O 1720
`Citizenship: U.S.A.
`
`Michael J. Finney
`489 Douglass Street
`San Francisco, CA 94114
`Citizenship: U.S.A.
`
`Assignee:
`
`MJ Research
`590 Lincoln Street
`Waltham, MA, 02451
`
`Entity:
`
`Small
`
`TOWNSEND and TOWNSEND and CREW LLP
`Two Embarcadero Center, gth Floor
`San Francisco, California 94111-3834
`Tel: 415-576-0200
`
`Agilent Exhibit 1204
`Page 10 of 224
`
`

`

`Attorney Docket No.: 021766-000lOOUS
`
`PATENT
`
`SYSTEMS AND METHODS FOR FLUORESCENCE DETECTION
`
`WITH A MOVABLE DETECTION MODULE
`
`5
`
`BACKGROUND OF THE INVENTION
`
`(0001] The present invention relates in general to fluorescence detection systems and in
`
`particular to a fluorescence detection system having a movable excitation/detection module
`
`for use with a thermal cycler.
`
`(0002] Thermal cyders are known in the art. Such devices are used in a variety of
`
`IO
`
`processes for creation ,and detection of various molecules of interest, e.g., nucleic acid
`
`sequences, in research, medical, and industrial fields. Processes that can be performed with
`
`conventional thermal cyders include but are not limited to amplification of nucleic acids
`
`using procedures such as the polymerase chain reaction (PCR). Such amplification processes
`
`are used to increase the amount of a target sequence present in a nucleic acid sample.
`
`15
`
`(0003] Numerous techniques for detecting the presence and/or concentration of a target
`
`molecule in a sample processed by a thermal cycler are also known. For instance, fluorescent
`
`labeling may be used. A fluorescent label (or fluorescent probe) is generally a substance
`
`which, when stimulated by an appropriate electromagnetic signal or radiation, absorbs the
`
`radiation and emits a signal (usually radiation that is distinguishable, e.g., by wavelength,
`
`20
`
`from the stimulating radiation) that persists while the stimulating radiation is continued, i.e. it
`
`fluoresces. Some types of fluorescent probes are generally designed to be active only in the
`
`presence of a target molecule (e.g., a specific nucleic acid sequence), so that a fluorescent
`
`response from a sample signifies the presence of the target molecule. Other types of
`
`fluorescent probes increase their fluorescence in proportion to the quantity of double-stranded
`
`25
`
`DNA present in the reaction. These types of probes are typically used where the
`
`amplification reaction is designed to operate only on the target molecule.
`
`[0004] Fluorometry involves exposing a sample containing the fluorescent label or probe to
`
`stimulating (also called excitation) radiation, such as a light source of appropriate
`
`wavelength, thereby exciting the probe and causing fluorescence. The emitted radiation is
`
`30
`
`detected using an appropriate detector, such as a photodiode, photomultiplier, charge-coupled
`
`device (CCD), or the like.
`
`Agilent Exhibit 1204
`Page 11 of 224
`
`

`

`[0005] Fluorometers for use with fluorescent-labeled samples are known in the art. One
`
`type of fluorometer is an optical reader, such as described by Andrews et al. in U.S. Patent
`
`No. 6,043,880. A sample plate containing an array of samples is inserted in the optical
`
`reader, which exposes the samples to excitation light and detects the emitted radiation. The
`
`5
`
`usefulness of optical readers is limited by the need to remove the sample plate from the
`
`thermal cycler, making it difficult to monitor the progress of amplification.
`
`[0006] One improvement integrates the optical reader with a thermal cycler, so that the
`
`sample plate may be analyzed without removing it from the thermal cycler or interrupting the
`
`PCR process. Examples of such combination devices are described in U.S. Patent No.
`
`10
`
`5,928,907, U.S. Patent No. 6,015,674, U.S. Patent No. 6,043,880, U.S. Patent No. 6,144,448,
`
`U.S. Patent No. 6,337,435, and U.S. Patent No. 6,369,863. Such combination devices are
`
`useful in various applications, as described, e.g., in U.S. Patent No. 5,210,015, U.S. Patent
`
`No. 5,994,056, U.S. Patent No. 6,140,054, and U.S. Patent No. 6,174,670.
`
`[0007] Existing fluorometers suffer from various drawbacks. For instance, in some
`
`15
`
`existing designs, different light sources and detectors are provided for different sample wells
`
`in the array. Variations among the light sources and/or detectors lead to variations in the
`
`detected fluorescent response from one well to the next. Alternatively, the light source and/or
`
`detector may be arranged in optical communication with more than one of the wells, with
`
`different optical paths to and/or from each well. Due to the different optical paths, the
`
`20
`
`detected fluorescent response varies from one sample well to the next. To compensate for
`
`such variations, the response for each sample well must be individually calibrated. As the
`
`number of sample wells in an array increases, this becomes an increasingly time-consuming
`
`task, and errors in calibration may introduce significant errors in subsequent measurements.
`
`[0008]
`
`In addition, existing fluorometers generally are designed such that the light sources
`
`25
`
`and detectors are fixed parts of the instrument. This limits an experimenter's ability to adapt
`
`a fluorometer to a different application. For instance, detecting a different fluorescent label
`
`generally requires using a different light source and/or detector. Many existing fluorometers
`
`make it difficult for an experimenter to reconfigure light sources or detectors, thus limiting
`
`the variety of fluorescent labels that may be used.
`
`30
`
`[0009]
`
`It is also difficult to perform concurrent measurements of a number of different
`
`fluorescent labels that may be present in a sample (or in different samples). As described
`
`above, to maximize the data obtained in an assay, experimenters often include multiple
`
`2
`
`Agilent Exhibit 1204
`Page 12 of 224
`
`

`

`fluorescent labeling agents that have different excitation and/or emission wavelengths. Each
`
`labeling agent is adapted to bind to a different target sequence, in principle allowing multiple
`
`target sequences to be detected in the same sample. Existing fluorometers, however, do not
`
`facilitate such multiple-label experiments. Many fluorometers are designed for a single
`
`5
`
`combination of excitation and emission wavelengths. Others provide multiple light sources
`
`and detectors to allow detection of multiple labels; however, these configurations often allow
`
`only one label to be probed at a time because the excitation wavelength of one label may
`
`overlap the emission wavelength of another label; excitation light entering the detector would
`
`lead to incorrect results. Probing multiple labels generally cannot be done in parallel,
`
`10
`
`slowing the data collection process.
`
`(0010] Therefore, an improved fluorometer for a thermal cycler that overcomes these
`
`disadvantages would be desirable.
`
`BRIEF SUMMARY OF THE INVENTION
`
`15
`
`[0011] Embodiments of the present invention provide fluorescence detection in a thermal
`
`cycling apparatus. According to one aspect of the invention, a fluorescence detection
`
`apparatus for analyzing samples located in a plurality of wells in a thermal cycler includes a
`
`support structure attachable to the thermal cycler and a detection module movably mountable
`
`on the support structure. The detection module includes an excitation light generator and an
`
`20
`
`emission light detector, both disposed within the detection module. When the support
`
`structure is attached to the thermal cycler and the detection module is mounted on the support
`
`structure, the detection module is movable so as to be positioned in optical communication
`
`with different ones of the plurality of wells.
`
`[0012] According to another aspect of the invention, the detection module may include two
`
`25
`
`or more excitation light generators and two or more emission light detectors arranged to form
`
`two or more excitation/detection pairs. In one embodiment, the excitation/detection pairs are
`
`arranged such that each excitation/detecti