Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 12/04/2023 and 07/16/2024 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-20 is/are rejected under 35 U.S.C. 103 as being obvious over Delattre et. al. (US 2019/0351413 effective filing date 5/15/2018, cited on 12/4/2023 IDS) in view of Banerjee et. al. (EP3373174, published 3/30/2007, cited in parent app IDS of 2/12/21).
The applied reference (i.e., Delattre et al) has a common Assignee (Illumina, Inc.) with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2).
This rejection under 35 U.S.C. 103 might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C.102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B); or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement. See generally MPEP § 717.02.
Claim interpretation: Instant claims are drawn to a method using specific
reagents and system components. The “reagent management system” recited in
generality has been interpreted as encompassed by any type of fluidic system capable
of performing the claimed steps.
Also, instant claims recited with alternate claim language “or” and “and/or” has
been interpreted to require single limitation.
With regard to the order of steps the courts have ruled that the selection of any
order of performing process steps is prima facie obvious in the absence of new or
unexpected results (In re Burhans, 154 F.2d 690, 69 USPQ 330 (CCPA 1946; In re
Gibson, 39 F.2d 975, 5 USPQ 230 (CCPA 1930; MPEP 2144.04 section IV C). In the
instant case, As discussed below Delattre in view of Banerjee teaches the system
components and the claimed steps and thus is prima facie obvious in the absence of
new or unexpected results.
Regarding claims 1-14, Delattre teaches in figure 3 and its associated
descriptions in the text, an instrument 100 that includes a flow cell 102 in fluid
communication with a reagent management system (RMS) 104, wherein the RMS 104
and the flow cell 102 are mechanically and flexibly connected together by a flexible
connection 106. The RMS 104 is capable of selecting and routing a plurality of reagents
108, 109, 110, 111, 112, 114, 116 and 118 flow through the flow channel and be routed
over the analytes 140 in order to perform various controlled chemical reactions on the
analytes with a predetermined sequence of the reagents 108-118. Delattre also teaches
that a chemical reaction between a reagent and analytes in a flow cell is where a
reagent delivers an identifiable label (such as a fluorescently labeled nucleotide molecule or the like) that may be used to tag the analytes. Thereafter, an excitation light may be radiated through the top layer of the flow cell or any other portion of the flow cell) and to the analytes, causing the fluorescent label tagged to the analytes to fluoresce emissive light photons. The emissive light photons may be scanned and/or detected by a detection module 126 (such as an imaging module) of the instrument 100 during a detection process (paragraphs [0146]- [0148]).
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Delattre further teaches that the reagents 108-118 may be any of several types
or combinations of reagents depending on the type and sequence of the chemical
reactions that are to be performed at the flow cell and further teaches that the reagents
108-118 may be of the following types: reagent 108 and 109 may be different
formulations of an incorporation mix, which is a mixture of chemicals that incorporates
fluorescently-labeled nucleotides into DNA strands, reagent 110 and 111 may be
different formulations of a scan mix, which is a mixture of chemicals that stabilize DNA
strands during a detection process, reagent 112 may be a cleave mix, which is a mixture of chemicals that enzymatically cleave fluorescently- labeled nucleotides from DNA strands and reagent 114 and 116 may be different formulations of a wash buffer, which is a mixture of wash reagents to remove the active reagents from a flow cell.
Delattre also teaches that one or more examples are illustrated in the
accompanying drawings and those skilled in the art will understand that the methods,
systems, and devices specifically described herein and illustrated in the accompanying
drawings are non-limiting examples and that the scope of the present disclosure is
defined solely by the claims. The features illustrated or described in connection with one
example maybe combined with the features of other examples. Such modifications and
variations are intended to be included within the scope of the present disclosure
(paragraph [0041]).
Delattre does not specifically teach the steps of flowing a buffer reagent, through
the reagent management system and flow cell in a plurality of cycles of consecutive
forward and reverse flow directions, which is taught Banerjee who is in the same field of
endeavor teaches systems and devices for sequencing one or more polynucleotide and
further teaches a fluid flow sub system also flows the appropriate reagents to remove the
blocked 3' terminus (if appropriate) and the fluorophore from each incorporated base,
wherein the fluid direction system that controllably moves various reagents (e.g.,
buffers, enzymes, fluorescently labeled nucleotides or oligonucleotides, etc.) into
contact with the polynucleotides; a temperature control system that regulates the
temperature of the substrate and/or of the reagents (paragraph [0007]) and further
teaches that the substrate can be exposed either to a second round of the four blocked
nucleotides, or optionally to a second round with a different individual nucleotide. Such cycles are then repeated and the sequence of each cluster is read over the multiple chemistry cycles. The computer aspect of the current invention can optionally align the sequence data gathered from each single molecule, cluster or bead to determine the sequence of longer polymers. Alternatively, the image processing and alignment can be performed on a separate computer (Banerjee, paragraph [0026]), thus providing teachings, suggestions and motivations to include fluid direction system that moves buffers and other reagents into contact with the polynucleotides for multiple chemistry cycles of Banerjee in the method of Delattre for sequencing longer polymers (i.e., polynucleotides), thus providing teachings, suggestions and motivation to include fluid direction system that moves buffers and other reagents into contact with the polynucleotides for multiple chemistry cycles polynucleotide in the method of Delattre.
The artisan would recognize that to combine the fluid direction system that
moves buffers and other reagents into contact with the polynucleotides for multiple
chemistry cycles of Banerjee with the method of Delattre, some routine optimization is
needed, which is within the skills of one having ordinary skill in the art.
It would have been prima facie obvious to one of ordinary skill in the art before
the effective filing date of the claimed invention to include the fluid direction system that
moves buffers and other reagents into contact with the polynucleotides for multiple
chemistry cycles of Banerjee in the method of Delattre with a reasonable expectation of
success with the expected benefit of increasing the longer polynucleotide sequencing
as taught by Banerjee. An artisan having ordinary skill in the art would have reasonable
expectation of success because it merely involves including missing steps which is
routinely practiced in the art as exemplified by Banerjee.
Based on the teachings of Delattre in view of Banerjee as discussed above
meets the limitation of claim 1 of “a method of flowing an incorporation reagent, through
a reagent management system and a flow cell of an instrument, the flow cell having a
first polynucleotide positioned therein, wherein the incorporation reagent adds a first
base onto a sequence of bases, the sequence of bases comprising a second
polynucleotide complementary to the first polynucleotide; capturing an image, of an
identification signal emanating from the first base, after the first base has been added
onto the second polynucleotide; flowing a cleavage reagent, through the reagent
management system and flow cell, to remove a first terminator from the first base in
order to enable a subsequent base in the sequence of bases to be added to the second
polynucleotide; and flowing a buffer reagent, through the reagent management system
and flow cell in a plurality of cycles of consecutive forward and reverse flow directions”.
Regarding dependent claims 2 and 3, Delattre teaches in paragraphs [0068]- [0072]
the type of reagents necessary to sequence the DNA strands, which include different
formulations of nucleotide incorporation mix that incorporates fluorescently-labeled
nucleotides into DNA strands and further teaches scan mix, cleave mix and wash mix,
which are necessary to sequence the DNA strand. Delattre further teaches the reagent may be different formulations of a wash buffer, which is a mixture of wash reagents to remove the active reagents from a flow cell. Banerjee teaches sequencing cycles can be about 25 to 50 cycles (Banerjee, paragraph [0156]).
The artisan would recognize that the limitations of plurality of cycles comprises 4
to 12 cycles are mere duplication steps and thus would be obvious over Delattre in view
of Banerjee.
Regarding claims 4 and 5, Delattre teaches the limitation of said claims in
paragraph [0012].
Regarding limitations of claims 6-14, Delattre teaches that the instrument 100
may include, among other things, one or more processors 176 that are to execute
program instructions stored in a memory 178 in order to perform the microfluidics
analysis operations. The processors are in electronic communication to a rotary valve
drive assembly 180, a syringe pump drive assembly 182, a pinch valve drive assembly
184, the detection module 126 and a movable temperature regulation assembly 206. A
user interface 186 is provided for users to control and monitor operation of the
instrument 100. A communications interface 188 can convey data and other information
between the instrument 100 and remote computers, networks and the like (Fig.3, [0093], [0094]).
Regarding claim 15, Delattre teaches an instrument comprising a reagent management system, positioned in the instrument ,the reagent management system comprising a plurality of reagent wells, the reagent wells having at least a first, a second and a third reagent well operable to contain an incorporation reagent ([0044]), a cleavage reagent and a buffer reagent positioned respectively therein ([0071], [0072]), the reagent management system to select a flow of reagent from one of the plurality of reagent wells; and a flow cell, positioned in the instrument, the flow cell comprising a flow channel in fluid communication with the reagent management system, the flow channel to route the flow of reagent over a first polynucleotide positioned in the flow channel; ([0074]) wherein the instrument is operable to: flow the incorporation reagent, through the reagent management system and flow cell, to add a first base onto a sequence of bases, the sequence of bases comprising a second polynucleotide complementary to the first polynucleotide ([0046]); capture an image, of an identification signal emanating from the first base, after the first base has been added onto the second polynucleotide; flow the cleavage reagent, through the reagent management system and flow cell, to remove a first terminator from the first base in order to enable a subsequent base in the sequence of bases to be added to the second polynucleotide; and flow the buffer reagent, through the reagent management system and flow cell in a plurality of cycles of consecutive forward and reverse flow directions ([0146]-[0148]).
The artisan having ordinary skill in the art would recognize that the teachings of
Delattre in view Banerjee taken in their entirety and common knowledge in the nucleic
acid sequencing field the limitations of claims 6-14 would be obvious for the reasons
discussed above.
Claims 1-20 are rejected under 35 U.S.C. 103 as being unpatentable over
Banerjee et al (EP3373174, published 3/30/2007, as cited above).
Regarding claim 1, Banerjee teaches a method for sequencing nucleic acids
comprises (i) flowing reagents (e.g., buffers, enzymes (such as polymerase),
fluorescently labeled nucleotides, cleavage reagents) through a fluid direction system
and a flow cell, wherein the flow cell has nucleic acids, wherein the nucleic acids comprise DNA clusters and the reagents comprise bases having the fluorescent labels and a blocking moiety, each DNA cluster including a plurality of single-stranded DNA fragments having a common sequence, wherein the reagents incorporate at least one base onto the DNA fragments; (ii) illuminating the DNA clusters to excite the fluorescent labels of the bases; (iii) capturing an image of emitted fluorescence from the DNA clusters; (iv) identifying the base incorporated onto the DNA fragments of the DNA clusters; (v) cleaving and removing the fluorescent labels and the blocking moiety(a terminator) from the bases by the cleavage reagents; and (vi) repeating steps (i)-(v) by using the reagents to determine the sequences of the DNA fragments; and (B) a device for sequencing the nucleic acids comprises the flow cell, reagent containers, and the fluid direction system, wherein the flow cell has at least one fluidic channel comprising the nucleic acids, wherein the reagent containers comprise the reagents, and wherein the fluid direction system moves the reagents into contact with the nucleic acids (see paragraphs [0010], [0016], [0025], [0026], [0044]-[0046], [0192]-[0204]; claims 1-15; figures 4A-7C, the components required for sequencing the nucleic acid).
The artisan having ordinary skill in the art would recognize that the teachings
of Banerjee of fluid direction system as discussed above meets the limitations of the recited
“Reagent management system”.
Regarding claims 2 and 3, Banerjee teaches sequencing cycles can be about 25
to 50 cycles (Banerjee, paragraph [0156]).
Regarding claims 4-20, Banerjee teaches computer system (paragraphs [0144]-
[0150]) and Exemplary use and Component Variation section (paragraphs [0151]- [0165])
teaches to optimize the flow rate (paragraph [0049]). The artisan would recognize that
the limitations of claims 4-20 would amount to routine optimization and thus would be obvious, barring any secondary consideration, over the teachings of Banerjee and common knowledge in the field of nucleic acid technology and thus would be obvious barring any secondary consideration.
Double Patenting
A rejection based on double patenting of the “same invention” type finds its support in the language of 35 U.S.C. 101 which states that “whoever invents or discovers any new and useful process... may obtain a patent therefor...” (Emphasis added). Thus, the term “same invention,” in this context, means an invention drawn to identical subject matter. See Miller v. Eagle Mfg. Co., 151 U.S. 186 (1894); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Ockert, 245 F.2d 467, 114 USPQ 330 (CCPA 1957).
A statutory type (35 U.S.C. 101) double patenting rejection can be overcome by canceling or amending the claims that are directed to the same invention so they are no longer coextensive in scope. The filing of a terminal disclaimer cannot overcome a double patenting rejection based upon 35 U.S.C. 101.
Claims 1-20 is/are rejected under 35 U.S.C. 101 as claiming the same invention as that of claims 1-20 of prior U.S. Patent No. 11911765. This is a statutory double patenting rejection.
Claims 1-20 of the instant application are anticipated by claims 1-20 of the reference because the claim language is identical.
Regarding claim 1, the language of instantly rejected claim 1 is identical to that of reference claim 1.
Regarding claim 2, the language of instantly rejected claim 2 is identical to that of reference claim 2.
Regarding claim 3, the language of instantly rejected claim 3 is identical to that of reference claim 3.
Regarding claim 4, the language of instantly rejected claim 4 is identical to that of reference claim 4.
Regarding claim 5, the language of instantly rejected claim 5 is identical to that of reference claim 5.
Regarding claim 6, the language of instantly rejected claim 6 is identical to that of reference claim 6.
Regarding claim 7, the language of instantly rejected claim 7 is identical to that of reference claim 7.
Regarding claim 8, the language of instantly rejected claim 8 is identical to that of reference claim 8.
Regarding claim 9, the language of instantly rejected claim 9 is identical to that of reference claim 9.
Regarding claim 10, the language of instantly rejected claim 10 is identical to that of reference claim 10.
Regarding claim 11, the language of instantly rejected claim 11 is identical to that of reference claim 11.
Regarding claim 12, the language of instantly rejected claim 12 is identical to that of reference claim 13, aside from claim numbering.
Regarding claim 13, the language of instantly rejected claim 13 is identical to that of reference claim 14, aside from claim numbering.
Regarding claim 14, the language of instantly rejected claim 14 is identical to that of reference claim 12, aside from claim numbering.
Regarding claim 15, the language of instantly rejected claim 15 is identical to that of reference claim 15. Reference claim 15 recites the additional limitation “to remove the cleavage reagent from the flow cell” at the end of par.7, line 25. The addition of this element does not significantly change the scope of the independent claim.
Regarding claim 16, the language of instantly rejected claim 16 is identical to that of reference claim 16.
Regarding claim 17, the language of instantly rejected claim 17 is identical to that of reference claim 17.
Regarding claim 18, the language of instantly rejected claim 18 is identical to that of reference claim 18.
Regarding claim 19, the language of instantly rejected claim 19 is identical to that of reference claim 19.
Regarding claim 20, the language of instantly rejected claim 20 is identical to that of reference claim 20.
Conclusion
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/A.H.B./Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
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