Office Action 3: Non-Final Rejection (2023-11-21)
Rejection types: 103 - Obviousness, Double Patenting

CLAIMS:
IN THE CLAIMS

The following listing of claims replaces all prior versions and listings of claims in the instant application.

Appl. No.: 16/535,565

1-20. (Canceled)219

21\. (Currently Amended) An apparatus comprising:
a flow cell;
a plurality of reservoirs fluidically coupled to the flow cell, the plurality of reservoirs configured to respectively hold four different nucleotide species;
a sensor operably coupled to the flow cell, the sensor being configured to sense one or more signals produced from incorporation of a nucleotide species of the four different nucleotide species into a polynucleotide in the flow cell; and
a fluidics controller operably coupled to the plurality of reservoirs, the fluidics controller configured to individually control flow from the plurality of reservoirs to provide a series of nucleotide flows to the flow cell,
wherein the series of nucleotide flows comprises a nucleotide flow sequence meeting predefined criteria such that the nucleotide flow sequence includes:each of the four different nucleotide species,
no consecutive repeat of any of the four different nucleotide species, and
an order such that three different nucleotide species of the four different nucleotide species occur before a fourth nucleotide species of the four different nucleotide species, and such that one or more of the three different nucleotide species occurs at least twice before the fourth nucleotide species,
wherein the series of nucleotide flows includes one or more consecutive repeats of the nucleotide flow sequence.
22\. (Previously Presented) The apparatus of claim 21, wherein the flow cell comprises a plurality of reaction sites, the plurality of reaction sites comprising a reaction site associated with the polynucleotide.

23\. (Previously Presented) The apparatus of claim 22, wherein the plurality of reaction sites comprise a plurality of microwells.
24\. (Previously Presented) The apparatus of claim 22, wherein the apparatus comprises a plurality of sensors, the plurality of sensors comprising the sensor, the plurality of sensors aligned with the plurality of reaction sites, and each sensor of the plurality configured to sense one or more signals produced from incorporation of the nucleotide species at a corresponding reaction site.
25\. (Previously Presented) The apparatus of claim 21, wherein the sensor is configured to sense pH.
26\. (Previously Presented) The apparatus of claim 21, wherein the sensor comprises a field effect transistor (FET).
27\. (Previously Presented) The apparatus of claim 21, wherein the sensor is configured to sense one or more signals produced from incorporation each of the four different nucleotide species into the polynucleotide.
28\. (Previously Presented) The apparatus of claim 21, wherein the apparatus comprises a plurality of sensors, the plurality of sensors comprising the sensor, each sensor of the plurality configured to sense one or more signals produced from incorporation of the nucleotide species.
29\. (Previously Presented) The apparatus of claim 21, wherein the sensor is one of a plurality of sensors of a sensor array, and the apparatus further comprises a semiconductor substrate, the semiconductor substrate comprising the sensor array.
30\. (Previously Presented) The apparatus of claim 21, further comprising a reference electrode operatively coupled to the sensor.
31\. (Previously Presented) The apparatus of claim 21, wherein the polynucleotide is coupled to a support.

32\. (Previously Presented) The apparatus of claim 31, wherein the support comprises a bead in the flow cell.
33\. (Previously Presented) The apparatus of claim 31, wherein the support is operatively coupled to the sensor.
34\. (Previously Presented) The apparatus of claim 21, further comprising a valve block fluidically coupling the plurality of reservoirs and the flow cell, the fluidic controller operably coupled to control the valve block.
35\. (Previously Presented) The apparatus of claim 21, wherein two or more of the three different nucleotide species occur at least twice before the fourth different nucleotide species is flowed in the nucleotide flow sequence.
36\. (Previously Presented) The apparatus of claim 21, wherein all three of the three different nucleotide species occur at least twice before the fourth different nucleotide species is flowed in the nucleotide flow sequence.
37\. (Previously Presented) The apparatus of claim 21, wherein one or more of the three different nucleotide species occurs at least three times before the fourth different nucleotide species is flowed in the nucleotide flow sequence.
38\. (Previously Presented) The apparatus of claim 21, wherein a first and second different nucleotide species of the three different nucleotide species occur at least twice and a third nucleotide species of the three different nucleotide species occurs at least three times before the fourth different nucleotide species is flowed in the nucleotide flow sequence.
39\. (Previously Presented) The apparatus of claim 21, wherein two or more of the three different nucleotide species occur at least three times before the fourth different nucleotide species is flowed in the nucleotide flow sequence.
40\. - 50. (Canceled)4149

OFFICE ACTION:
DETAILED ACTION
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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection.  Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.  Applicant's submission filed on 10/30/2023 has been entered.
Application Status
This action is written in response to applicant’s correspondence received 10/30/2023.  Claims 21-39 are currently pending.  Claims 1-20 and 40-50 have been cancelled.  Claims 21-39 are presently under examination in this office action.
Any Rejection or objection not reiterated herein has been overcome by amendment.  Applicant’s arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary.  Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 21-39 are rejected under 35 U.S.C. 103 as being unpatentable over Rothberg (US 2009/0127589) in view of Garcia (Garcia et al. (2000) Gene, 253:249-257), GenBank FJ883007 (NCBI Database accession number: FJ883007, portion of the coding region of Cercopithecine herpesvirus 5, 2 pages, published 2009), and Alcendor (Alcendor DJ et al. Virology. 2009 Dec 5;395(1):21-32).
Regarding claim 21, Rothberg teaches an apparatus for the sequencing-by-synthesis of a polynucleotide strand (see [0124] and FIG. 8). In Fig. 8, Rothberg illustrates that it comprises a flow cell (200), a plurality of reservoirs (272) fluidically coupled to the flow cell and configured to hold dATP, dCTP, dGTP, and dTTP (i.e. four different nucleotide species), an ISFET array (100) (i.e. a sensor), and pumps (274) and valves (270) controlled by a computer (260) to individually control flow from the plurality of reservoirs (272) to provide a series of nucleotide flows to the flow cell (i.e. a fluidics controller) (see FIG. 8).
Regarding the ISFET array, Rothberg teaches that it comprises an “array” of “sensor elements” ([0015]) that facilitate measurement of the hydrogen ion concentration of a solution, commonly denoted as pH ([0003]). Rothberg teaches ISFET is a particular type of chemFET that is configured for ion detection ([0029]). Rothberg teaches that a new strand is synthesized by incorporating one or more of four different nucleotide triphosphates at the 3’ end of the sequencing primer, which is then detected by the chemFET ([0051] and [0122]).
Regarding the series of nucleotide flows, Rothberg teaches that the nucleotides are provided from the multiple reservoirs to the flow chamber in any sequential order ([0334]), and therefore teaches that the fluidics controller is programmed to successively provide nucleotide flows according to a predetermined ordering. Rothberg teaches a four nucleotide flow ordering of dATP, dCTP, dGTP, and dTTP, which can be repeated any number of times ([0335]), and therefore teaches a flow ordering that contains each of the four different nucleotide species, there is no consecutive repeat of any of the four different nucleotide species, and an order such that three different nucleotide species (e.g. dATP, dCTP, dGTP) occur before a fourth nucleotide species (e.g. dTTP).
However, Rothberg does not teach that one or more of the three different nucleotide species occurs at least twice before the fourth nucleotide species, and that this nucleotide flow sequence would be consecutively repeated at least once.
However, Rothberg does teach that the apparatus is intended to be used for the for sequencing-by-synthesis applications ([0124]) and further for the detection of mutations in certain genes such as deletions, additions, substitutions, and single nucleotide polymorphisms ([0353]).
In addition, Garcia teaches that pyrosequencing is a method for the sequencing-by-synthesis of a polynucleotide strand useful for the detection of mutations by sequencing (see abstract and page 250, column 1, paragraph 1). Garcia teaches using a pyrosequencer apparatus (see page 250, column 2, last paragraph) that was programmed to successively deliver nucleotides to a polynucleotide template according to a customized programmed nucleotide dispensation order (i.e. a series of nucleotide flows) to detect mutations in the p53 gene (see Figure 4), as follows: A-G-T-C-T-G-A-G-A-G-A-C-G-C-G-C-A. Within this series of nucleotide flows that comprises a flow sequence of T-G-A-G-A-G-A-C, which comprises each of the four different nucleotide species, there are no consecutive repeats of any of the four different nucleotide species, and it contains an order in which T, G, and A (i.e. three different nucleotide species) occur before C (i.e. the fourth nucleotide species), and G and A (i.e. one or more of the three different nucleotide species) occur three times (i.e. at least twice) before C (i.e. the fourth nucleotide species).  Furthermore, Garcia teaches that there are advantages to using programmed nucleotide dispensation when sequencing, stating that this approach leads to “longer and faster reads, and fewer out-of-phase problems”, Abstract.  Thus, Garcia teaches that their method can be applied to sequencing in general with improved results including longer, fast reads and also corrects phase problems which occur when sequencing.
As discussed above, Garcia teaches sequencing the p53 gene, but the specific sequence recited in their article is not repeated consecutively during the sequencing process.  GenBank FJ883007, a portion of the genomic sequence of the cercopithecine herpesvirus 5 virus, teaches that the sequence “T-G-T-G-A-G-A-T-A-C” occurs successively at position 546 (GenBank FJ883007, second page, beginning at position 546).  Thus, a practitioner sequencing this herpesvirus using the predetermined/programmed nucleotide dispensation nucleotide flow technique taught by Garcia would flow the series “T-G-T-G-A-G-A-T-A-C” twice (consecutively) during the sequencing process taught by Garcia.  The sequence “T-G-T-G-A-G-A-T-A-C” contains each of the four different nucleotide species, no consecutive repeats of any of the four different nucleotide species, and an order where three different nucleotide species occur before the fourth nucleotide species where one or more of the three occurs twice (“A”, “G”, and “T” occur three times before “C”).
Furthermore, GenBank FJ883007 was uploaded in connection with the research article taught by Alcendor in 2009.  Alcendor teaches patterns of viral divergence in cytomegalovirus genomes (Abstract, throughout) where GenBank FJ883007 is one such virus (see page 1 of GenBank FJ883007, which indicates that the viral sequence was uploaded in conjunction with Alcendor).  Additionally, Alcendor references GenBank accession number FJ883007 directly (page 11, “GenBank accession numbers”, line 2) as one of the viral sequences which they sequenced.   Furthermore, Alcendor teaches that:
“Although the functions of most primate CMV vCXCLs and vGPCRs are unknown, most of them are dispensible in fibroblast cell cultures. Nonetheless, in our opinion, each paralog is likely to have its own role during infection in vivo, whether as a chemokine or as some other function. The limited information available points to a role in virus spread and dissemination in vivo for HCMV UL146 vCXCL, which binds in a species-specific fashion to human CXCLR2”, Introduction, fourth paragraph,
and
“we have compared the organization of the two clusters with those in other known primate CMVs, and attempted to deduce some of the duplication and deletion events that might have occurred during their capture and subsequent divergent evolution into the different viral lineages”, Introduction, final sentence.
Alcendor therefore teaches that more information of CMV viruses is required to understand their in vivo infection mechanisms, as there is limited information currently available for these viruses.  Alcendor further teaches that such information could be useful in understanding viral “spread” and “dissemination” in vivo for human cytomegaloviruses (HCMV) (Introduciton, fourth paragraph, above).  Thus, Alcendor teaches a motivation to sequence CMV viral genomes, including GenBank FJ883007 for the purposes of comparative viral evolutionary analysis.
It would have been obvious to one of ordinary skill in the art at the time the invention was made to modify Rothberg’s pyrosequencing method by delivering nucleotides according to a predetermined ordering of Garcia because it would have merely required combining known elements according to known methods to yield predictable results. One would have been motivated to combine Rothberg and Garcia to properly and accurately sequence the p53 gene taught by Garcia, which has been associated with cancer, as taught by Garcia. It would have been predictable to do so because Rothberg teaches that the apparatus is intended to be used for sequencing-by-synthesis applications ([0124]) and further teaches that the nucleotides may be delivered in any order ([0334]), as discussed above.  Furthermore, Garcia teaches the additional motivation of using their pre-programmed/predetermined nucleotide dispensation flow sequence when sequencing in general because such a method improves the speed and read length of sequencing, and also corrects out-of-phase problems.  Therefore, the advantages of the sequencing method of Garcia can be broadly applied to sequencing of any organism.  As such, a practitioner would be further motivated to use the sequencing method of Garcia to sequence the cytomegalovirus taught by GenBank FJ883007 and Alcendor, as this was a known sequence, and Alcendor teaches motivation to sequence such viruses for comparative evolutionary biology purposes in order to better understand viruses which can infect humans.
Regarding claims 22 and 23, Rothberg teaches that the flow cell comprises a plurality of reaction chambers (i.e. reaction sites) comprising microwells ([0031]) that comprise a DNA template and sequencing primer (i.e. a polynucleotide) to which nucleotide triphosphates are sequentially incorporated ([0051] and [0124]).
Regarding claims 24 and 28, Rothberg teaches that the apparatus comprises a chemFET array (i.e. a plurality of sensors) comprising at least one chemFET (i.e. a sensor) for each reaction chamber for the plurality of reaction chambers that detect incorporation of the nucleotide triphosphates ([0051]). Regarding claim 24, Rothberg further describes the alignment between the plurality of sensors and the plurality of reaction sites ([0251] and [0254]).
Regarding claims 25 and 26, Rothberg teaches that the sensor comprises an ion sensitive field effect transistor (ISFET) ([0003]), that is configured to measure pH ([0033]).
Regarding claim 27, Rothberg teaches that the sensor is configured to sense signals produced from incorporation of each of the four different nucleotide species into the polynucleotide ([0051]).
Regarding claim 29, Rothberg teaches that operation of an ISET is based on modulation of charge concentration caused by metal-oxide-semiconductor (MOS) capacitance ([0006]) and further teaches that the CMOS-fabricated sensors comprise the chemFET array (see [0037]).
Regarding claim 30, Rothberg teaches that the apparatus further comprises a reference electrode operatively coupled with the ISFET array ([0126]).
Regarding claims 31-33, Rothberg teaches that the polynucleotide is coupled to a bead in the flow cell that is attached to a chemFET array having separate reaction chambers for each sensor, wherein only one bead is situated in each reaction chamber ([0058]).
Regarding claim 34, Rothberg teaches that the apparatus comprises computer-controlled valves (i.e. a valve block) that fluidically couples the plurality of reservoirs (272) comprising the four different nucleotide species with the flow cell (200), the computer (260) (i.e. fluidic controller) operably coupled to control the valve block (see FIG. 8).
Regarding claims 35-39, the sequence discussed above in the rejection of claim 21 found in GenBank FJ883007 (“T-G-T-G-A-G-A-T-A-C”) occurs consecutively (beginning at position 546 of GenBank FJ883007) and furthermore this sequence reads on the claim limitations set forth in claims 35-39.
Response to Arguments
Applicant's arguments filed 10/30/2023 have been fully considered but they are not persuasive. Applicant has amended independent claim 21 to specify that the series of nucleotide flows includes one or more consecutive repeats of the nucleotide flow sequence.  Applicant argues on page 7 of the remarks, second paragraph, that the previously recited prior art does not teach that the recited nucleotide flow sequences are “consecutive repeats”.  The Office maintains that the combination of Rothberg and Garcia arrives at alternative flow sequencing, and further The Office has expanded its search to include sequences which a practitioner would reasonably sequence which contain “consecutive” repeats which also adhere to the recited criteria of the claim limitations.  As a result, The Office argues that a practitioner would be motivated to sequence cytomegaloviruses such as those taught by Alcendor (see above), including the viral genome comprising the sequence taught in GenBank FJ883007 (above).  This sequence contains the sequence “T-G-T-G-A-G-A-T-A-C” consecutively:  this sequence reads on claims 21 and 35-39 and the limitations set forth in said claims.  Furthermore, The Office asserts that a practitioner would be motivated to sequence CMV viruses, to better understand viral lineages and evolutionary viral divergences, especially in light of the fact that Alcendor teaches a deficiency in such knowledge (see 103 rejection above). Furthermore, Alcendor’s sequencing of the CMV viruses discussed above alone is evidence that a virologist would be motivated to sequence such viruses.  As Garcia’s sequencing method is broadly applicable to sequencing strategies, and also has known advantages (above), a practitioner would be motivated to apply such sequencing strategies to a given sequence such as GenBank FJ883007.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA  as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/process/file/efs/guidance/eTD-info-I.jsp.
Claims 21-39 are rejected on the ground of non-statutory double patenting as being unpatentable over claims 1-17 of U.S. Patent No. 9,605,308.
The patented claims teach an apparatus for sequencing a polynucleotide strand comprising a flow chamber for receiving flows of different dNTP reagents, multiple reservoirs that contain a different dNTP, flow paths from each of the reservoirs to the flow chamber, and a fluidics controller that is programmed to successively provide flow from the multiple reservoirs to the flow chamber according to an alternate ordering (see patented claim 1). The patented claims teach that the alternate ordering comprises the same number of flows for each of four different dNTP reagent flows and comprises a flow of nucleotides N-W-N-Z and is successively repeated at least once (see patented claim 1). The patent’s specification teaches that a preferred nucleotide flow ordering is TACAT-ACGCA-CGTGC-GTATG (column 8, lines 1-5), and also includes claim language in claim 1 indicating that the flow sequence is repeated. The patent’s specification further describes the sequencing instrumentation (see columns 10-12), which further addresses the structural limitations of the current claims. These disclosures of the preferred alternate nucleotide sequence flow ordering and further the preferred structural features of the apparatus indicate that meet the limitations of the current claims indicates that the patented claims and the current claims each encompass overlapping subject matter.
Response to Arguments – Double Patenting
Applicant's arguments filed 10/30/2023 have been fully considered but they are not persuasive. The applicant has not provided an argument explaining why the recited claims are not instances of double patenting.  The non-statutory double patenting rejection is therefore maintained.
Conclusion

APPLICANT REBUTTAL: R
EMARKS
I.
Claim Status:
Claims 21 and 35-39 are amended. Claims 1-20 and 40-50 are cancelled. After the foregoing amendments are entered into the record, claims 21 - 39 will be pending in this case.
Support for the claim amendments can be found in the application as-filed, e.g., at paragraph [0034]. Thus, no new subject matter is added as a result of these amendments.
II.
Claim Re
j
ections Under 35 U.S.C.
Claims 21-39 are rejected under 35 U.S.C. 103 as being unpatentable over Rothberg (US 2009/0127589) in view of Garcia (Garcia et al. (2000) Gene, 253:249-257), GenBank FJ883007 (NCBI Database accession number: FJ883007, portion of the coding region of Cercopithecine herpesvirus 5, 2 pages, published 2009), and Alcendor (Alcendor DJ et al. Virology. 2009 Dec 5; 395(1):21 -32).
In response, while not necessarily agreeing with the grounds for the rejection and to advance
prosecution, Applicant has amended claim 21. Applicant respectfully traverses the rejection in view of the amended claim 21. With respect to Rothberg, the Office Action on page 5, 2nd paragraph, states, "However, Rothberg does not teach that one or more of the three different nucleotide species occurs at least twice before the fourth nucleotide species, and that this nucleotide flow sequence would be consecutively repeated at least once." With respect to Garcia, the Office Action on page 6, 2nd paragraph, states, "As discussed above, Garcia teaches sequencing the p53 gene, but the specific sequence recited in their article is not repeated consecutively during the sequencing process." With respect to GenBank FJ883007, the Office Action the Office Action on page 6, 2nd paragraph, states, "GenBank FJ883007, a portion of the genomic sequence of the cercopithecine herpesvirus 5 virus, teaches the sequence "T-G-T-G-A-G-A-T-A-C" occurs successively at position 546."
Claim 21, as amended, recites (emphasis added):
An apparatus comprising:
a flow cell;
a plurality of reservoirs fluidically coupled to the flow cell, the plurality of reservoirs
configured to respectively hold four different nucleotide species;
a sensor operably coupled to the flow cell, the sensor being configured to sense one or
more signals produced from incorporation of a nucleotide species of the four different nucleotide
species into a polynucleotide in the flow cell; and
a fluidics controller operably coupled to the plurality of reservoirs, the fluidics controller
configured to individually control flow from the plurality of reservoirs to provide a series of
nucleotide flows to the flow cell,
wherein the series of nucleotide flows comprises a nucleotide flow sequence meeting
predefined criteria such that the nucleotide flow sequence includes: each of the four different nucleotide species, no consecutively repeated nucleotide flow of any of the four different nucleotide species, and
a flow ordering such that three different nucleotide species of the four different nucleotide species are flowed before a fourth nucleotide species of the four different nucleotide
species is flowed, and such that one or more of the three different nucleotide species is flowed at
least twice before the fourth nucleotide species is flowed,
wherein the series of nucleotide flows includes one or more consecutive repeats of the nucleotide flow sequence, wherein the flow ordering comprises a same number of
nucleotide flows for each of the four different nucleotide species.
Applicant respectfully submits that the sequence "T-G-T-G-A-G-A-T-A-C" of GenBank FJ883007 does not necessarily represent a flow ordering. However, assuming, arguendo, that the sequence "T-G-T-G- A-G-A-T-A-C" would represent a flow ordering, it does not fulfill the criteria, "wherein the flow ordering comprises a same number of nucleotide flows for each of the four different nucleotide species," as required by claim 31. The sequence "T-G-T-G-A-G-A-T-A-C" contains 3 T's, 3 G's, 3 A's, and only 1 C.
For at least the above reasons, Applicant respectfully asserts that Rothberg in view of Garcia,
GenBank FJ883007, and Alcendor alone or in combination, do not teach or suggest all the limitations of claim 21. Applicant respectfully asserts that claim 21 is allowable over the cited references. Claims 22-39 depend from claim 21 and are allowable for at least the same reasons as claim 21.
Accordingly, Applicant respectfully requests reconsideration and withdrawal of the rejection of claims under 35 U.S.C. §103.
III.
Claim Re
j
ections Under Double Patenting:
Claims 21-39 are rejected on the ground of non-statutory double patenting as being unpatentable over
claims 1-17 of U.S. Patent No. 9,605,308.
Applicant respectfully requests that the non-statutory double patenting rejections be held in abeyance until a determination of allowable subject matter has been finally made in the instant application.
Conclusion

NEXT OFFICE ACTION: DETAILED ACTION
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 .
Application Status
This action is written in response to applicant’s correspondence received on 2/21/2024.  Claims 21-39 are pending. Claims 21 and 35-39 have been amended. Claims 1-20 and 40-50 have been cancelled.  All pending claims are currently under examination.
Any rejection or objection not reiterated herein has been overcome by amendment.  Applicant’s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow. This Office Action is Final.
Claim Rejections - 35 USC § 103 – New Rejections Necessitated by Amendment
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary.  Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 21-34 are rejected under 35 U.S.C. 103 as being unpatentable over Rothberg (US 2009/0127589) in view of Garcia (Garcia et al. (2000) Gene, 253:249-257), GenBank AL021938 (NCBI Database accession number: AL021938, portion of the coding region of the human JMJ protein, published 2008), and Kim (Kim TG et al. J Biol Chem. 2003 Oct 24;278(43):42247-55).
Regarding claim 21, Rothberg teaches an apparatus for the sequencing-by-synthesis of a polynucleotide strand (see [0124] and FIG. 8). In Fig. 8, Rothberg illustrates that it comprises a flow cell (200), a plurality of reservoirs (272) fluidically coupled to the flow cell and configured to hold dATP, dCTP, dGTP, and dTTP (i.e. four different nucleotide species), an ISFET array (100) (i.e. a sensor), and pumps (274) and valves (270) controlled by a computer (260) to individually control flow from the plurality of reservoirs (272) to provide a series of nucleotide flows to the flow cell (i.e. a fluidics controller) (see FIG. 8).
Regarding the ISFET array, Rothberg teaches that it comprises an “array” of “sensor elements” ([0015]) that facilitate measurement of the hydrogen ion concentration of a solution, commonly denoted as pH ([0003]). Rothberg teaches ISFET is a particular type of chemFET that is configured for ion detection ([0029]). Rothberg teaches that a new strand is synthesized by incorporating one or more of four different nucleotide triphosphates at the 3’ end of the sequencing primer, which is then detected by the chemFET ([0051] and [0122]).
Regarding the series of nucleotide flows, Rothberg teaches that the nucleotides are provided from the multiple reservoirs to the flow chamber in any sequential order ([0334]), and therefore teaches that the fluidics controller is programmed to successively provide nucleotide flows according to a predetermined ordering. Rothberg teaches a four nucleotide flow ordering of dATP, dCTP, dGTP, and dTTP, which can be repeated any number of times, and therefore teaches a flow ordering that contains each of the four different nucleotide species, there is no consecutive repeat of any of the four different nucleotide species, and an order such that three different nucleotide species (e.g., dATP, dCTP, dGTP) occur before a fourth nucleotide species (e.g., dTTP, [0335]).
However, Rothberg does not teach that one or more of the three different nucleotide species occurs at least twice before the fourth nucleotide species, and that this nucleotide flow sequence would be consecutively repeated at least once.  Rothberg also does not teach that the flow ordering comprises a same number of nucleotide flows for each of the four different nucleotide species.
However, Rothberg does teach that the apparatus is intended to be used for the for sequencing-by-synthesis applications ([0124]) such as for the detection of mutations in certain genes such as deletions, additions, substitutions, and single nucleotide polymorphisms ([0353]).
In addition, Garcia teaches that pyrosequencing is a method for the sequencing-by-synthesis of a polynucleotide strand useful for the detection of mutations by sequencing (see abstract and page 250, column 1, paragraph 1). Garcia teaches using a pyrosequencer apparatus (see page 250, column 2, last paragraph) that was programmed to successively deliver nucleotides to a polynucleotide template according to a customized programmed nucleotide dispensation order (i.e., a series of nucleotide flows) to detect mutations in the p53 gene (see Figure 4), as follows: A-G-T-C-T-G-A-G-A-G-A-C-G-C-G-C-A. Within this series of nucleotide flows that comprises a flow sequence of T-G-A-G-A-G-A-C, which comprises each of the four different nucleotide species, there are no consecutive repeats of any of the four different nucleotide species, and it contains an order in which T, G, and A (i.e. three different nucleotide species) occur before C (i.e. the fourth nucleotide species), and G and A (i.e. one or more of the three different nucleotide species) occur three times (i.e. at least twice) before C (i.e. the fourth nucleotide species).  Furthermore, Garcia teaches that there are advantages to using programmed nucleotide dispensation when sequencing, stating that this approach leads to “longer and faster reads, and fewer out-of-phase problems”, (Abstract).  Thus, Garcia teaches that their method can be applied to sequencing in general with improved results including longer, fast reads and also corrects phase problems which occur when sequencing (Abstract).
As discussed above, Garcia teaches sequencing the p53 gene, but the specific sequence recited in their article is not repeated consecutively during the sequencing process, nor does the flow ordering comprise a same number of flows for each of the four nucleotides.  GenBank AL021938 (‘938) is a portion of the human genome encoding the JMJ protein sequence (see top of page 2). ‘938  teaches that the sequence “A-G-A-T-C-G-T-C” occurs successively at position 7896 (GenBank FJ883007, see alignment on the first page).  The sequence “A-G-A-T-C-G-T-C” contains each of the four nucleotides, where the nucleotide “A” occurs twice before the fourth nucleotide (i.e., “C”), occurs twice in a row/consecutively, and also comprises the same number of each nucleotide (i.e., there are two As, Gs, Ts, and Cs).  Thus, a practitioner sequencing this region of the human genome using the predetermined/programmed nucleotide dispensation nucleotide flow technique taught by Garcia would flow the series “A-G-A-T-C-G-T-C” twice (consecutively) during the sequencing process taught by Garcia.  Furthermore, the sequence “A-G-A-T-C-G-T-C” contains each of the four different nucleotide species, no consecutive repeats of any of the four different nucleotide species, and an order where three different nucleotide species occur before the fourth nucleotide species where one or more of the three occurs twice (“A” occurs twice before “C”).
Kim teaches that the protein JUMONJI protein (i.e., JMJ) is a critical factor in cardiac development of mammals (Title, Abstract, and see document).  Kim teaches that JMJ is a functional transcriptional repressor in normal cardiac development, and further teaches that mutations in transcription factors are known to be associated with abnormal cardiac developments (Abstract and page 42247, right column third and fourth paragraphs).  Thus, Kim teaches that JMJ is an important protein for normal cardiac development, and further teaches that identifying mutations in JMJ may be important for determining abnormal cardiac development (Abstract, page 42247, right column, paragraphs 3-4).  Kim therefore teaches a motivation to sequence the JMJ gene (Title, Abstract, see document).
It would have been obvious to one of ordinary skill in the art at the time the invention was made to modify Rothberg’s pyrosequencing method by delivering nucleotides according to a predetermined ordering of Garcia because it would have merely required combining known elements according to known methods to yield predictable results. One would have been motivated to combine Rothberg and Garcia to properly and accurately sequence the p53 gene taught by Garcia, which has been associated with cancer, as taught by Garcia. It would have been predictable to do so because Rothberg teaches that the apparatus is intended to be used for sequencing-by-synthesis applications ([0124]) and further teaches that the nucleotides may be delivered in any order ([0334]), as discussed above.  Furthermore, Garcia teaches the additional motivation of using their pre-programmed/predetermined nucleotide dispensation flow sequence when sequencing in general because such a method improves the speed and read length of sequencing, and also corrects out-of-phase problems.  Therefore, the advantages of the sequencing method of Garcia can be broadly applied to sequencing of any organism.  As such, a practitioner would be further motivated to use the sequencing method of Garcia to sequence the JMJ protein of the human genome taught by GenBank AL021938 and Kim, as this was a known sequence, and Kim teaches motivation to sequence the JMJ protein to better understand cardiac development and to identify mutations which may lead to disease (Abstract, page 42247 right column, paragraphs 3-4). Furthermore, a practitioner would be inherently motivated to sequence the human genome for research and medical reasons such as personalized health.
Regarding claims 22 and 23, Rothberg teaches that the flow cell comprises a plurality of reaction chambers (i.e., reaction sites) comprising microwells ([0031]) that comprise a DNA template and sequencing primer (i.e. a polynucleotide) to which nucleotide triphosphates are sequentially incorporated ([0051] and [0124]).
Regarding claims 24 and 28, Rothberg teaches that the apparatus comprises a chemFET array (i.e., a plurality of sensors) comprising at least one chemFET (i.e., a sensor) for each reaction chamber for the plurality of reaction chambers that detect incorporation of the nucleotide triphosphates ([0051]). Regarding claim 24, Rothberg further describes the alignment between the plurality of sensors and the plurality of reaction sites ([0251] and [0254]).
Regarding claims 25 and 26, Rothberg teaches that the sensor comprises an ion sensitive field effect transistor (ISFET) ([0003]), that is configured to measure pH ([0033]).
Regarding claim 27, Rothberg teaches that the sensor is configured to sense signals produced from incorporation of each of the four different nucleotide species into the polynucleotide ([0051]).
Regarding claim 29, Rothberg teaches that operation of an ISET is based on modulation of charge concentration caused by metal-oxide-semiconductor (MOS) capacitance ([0006]) and further teaches that the CMOS-fabricated sensors comprise the chemFET array (see [0037]).
Regarding claim 30, Rothberg teaches that the apparatus further comprises a reference electrode operatively coupled with the ISFET array ([0126]).
Regarding claims 31-33, Rothberg teaches that the polynucleotide is coupled to a bead in the flow cell that is attached to a chemFET array having separate reaction chambers for each sensor, wherein only one bead is situated in each reaction chamber ([0058]).
Regarding claim 34, Rothberg teaches that the apparatus comprises computer-controlled valves (i.e., a valve block) that fluidically couples the plurality of reservoirs (272) comprising the four different nucleotide species with the flow cell (200), the computer (260) (i.e., fluidic controller) operably coupled to control the valve block (see FIG. 8).
Claims 21-38 are rejected under 35 U.S.C. 103 as being unpatentable over Rothberg (US 2009/0127589) in view of Garcia (Garcia et al. (2000) Gene, 253:249-257), GenBank CR382129 (NCBI Database accession number: CR382129, Yarrowia lipolytica genome published 2008), and Bankar (Bankar AV et al. Appl Microbiol Biotechnol. 2009 Oct;84(5):847-65).
A discussion of the teachings of Rothberg and Garcia are given above for claims 21-34.
The combination of Rothberg and Garcia does not teach that one or more of the three different nucleotide species occurs at least twice before the fourth nucleotide species, and that this nucleotide flow sequence would be consecutively repeated at least once.  Rothberg/Garcia also does not teach that the flow ordering comprises a same number of nucleotide flows for each of the four different nucleotide species.
Regarding claim 21, GenBank CR382129 teaches the sequence “A-C-T-C-T-C-A-G-T-G-A-G” occurs consecutively in the genome of Y. lipolytica beginning at position 1328178 (page 1 of GenBank CR382129).  The sequence “A-C-T-C-T-C-A-G-T-G-A-G” contains four different nucleotides (A, C, T, and G). Furthermore, this sequence contains three nucleotides before a fourth nucleotide (A,C, and T occur before G), where each of A, C, and T occur at least twice before G.  GenBank CR382129 teaches that this sequence occurs consecutively in Y. lipolytica (page 1).  This sequence contains an equal number of A, C, T, and G nucleotides (three of each).  The sequence “A-C-T-C-T-C-A-G-T-G-A-G” taught by GenBank CR382129 therefore reads on the flow ordering recited in claim 21.
Regarding claim 35, the sequence “A-C-T-C-T-C-A-G-T-G-A-G” taught by GenBank CR382129 contains two each of A, C, and T before the nucleotide G (page 1).
Regarding claim 36, the sequence “A-C-T-C-T-C-A-G-T-G-A-G” taught by GenBank CR382129 contains three nucleotides (A,C, and T) which occur at least twice before the fourth nucleotide G (page 1).
Regarding claim 37, the sequence “A-C-T-C-T-C-A-G-T-G-A-G” taught by GenBank CR382129 contains at least one nucleotide (“C”) which occurs three times before the fourth nucleotide (page 1).
Regarding claim 38, the sequence “A-C-T-C-T-C-A-G-T-G-A-G” taught by GenBank CR382129 contains two species of nucleotides (A and T) which occur twice before the fourth nucleotide, and one species of nucleotide (C) which occurs three times before the fourth nucleotide (page 1).
Furthermore, GenBank CR382129 teaches that the sequence “A-C-T-C-T-C-A-G-T-G-A-G-A-C-T-C-T-C-A-G-T-G-A-G” is part of the genome of Y. lipolytica (page 1). Bankar is a research article which teaches the industrial relevance of the yeast Y. lipolytica (Title, Abstract, and see entire document).  Bankar teaches that Y. lipolytica has the potential to play an important role in biotechnological applications (Abstract).  Bankar therefore teaches that Y. lipolytica is an industrially important microbe that should be studied (Abstract, page 856 final paragraph, Conclusions, and document as a whole).
It would have been obvious to one of ordinary skill in the art at the time the invention was made to modify Rothberg’s pyrosequencing method by delivering nucleotides according to a predetermined ordering of Garcia because it would have merely required combining known elements according to known methods to yield predictable results. One would have been motivated to combine Rothberg and Garcia to properly and accurately sequence the p53 gene taught by Garcia, which has been associated with cancer, as taught by Garcia. It would have been predictable to do so because Rothberg teaches that the apparatus is intended to be used for sequencing-by-synthesis applications ([0124]) and further teaches that the nucleotides may be delivered in any order ([0334]).  Furthermore, Garcia teaches the additional motivation of using their pre-programmed/predetermined nucleotide dispensation flow sequence when sequencing in general because such a method improves the speed and read length of sequencing, and also corrects out-of-phase problems (Abstract).  Therefore, the advantages of the sequencing method of Garcia can be broadly applied to sequencing of any organism.  As such, a practitioner would be further motivated to use the sequencing method of Garcia to sequence the Y. lypolytica genome taught by GenBank CR382129 and Bankar, as this was a known sequence, and Bankar teaches motivation to sequence the Y. lypolytica genome to better understand this commercially and industrially relevant microbe (Title, Abstract, Conclusions).  A practitioner would therefore flow the sequence “A-C-T-C-T-C-A-G-T-G-A-G-A-C-T-C-T-C-A-G-T-G-A-G” when sequencing the genome of Y. lypolytica using the sequencing method suggested by the teachings of Rothberg/Garcia, where this sequence reads on the flow ordering limitations of claims 21 and 34-38.
Claims 21-34, 37, and 39 are rejected under 35 U.S.C. 103 as being unpatentable over Rothberg (US 2009/0127589) in view of Garcia (Garcia et al. (2000) Gene, 253:249-257), GenBank AC133089 (NCBI Database accession number: AC133089, Mus musculus genome published 2004), and Grimwood (Grimwood J et al. Nature. 2004 Apr 1;428(6982):529-35).
A discussion of the teachings of Rothberg and Garcia are given above for claims 21-34.
The combination of Rothberg and Garcia does not teach that one or more of the three different nucleotide species occurs at least twice before the fourth nucleotide species, and that this nucleotide flow sequence would be consecutively repeated at least once.  Rothberg/Garcia also does not teach that the flow ordering comprises a same number of nucleotide flows for each of the four different nucleotide species.
Regarding claim 21, GenBank AC133089 teaches the sequence “G-T-G-T-G-T-C-A-C-A-C-A” occurs consecutively in the genome of M. musculus, chromosome 19, beginning at position 142467 (page 1 of GenBank AC133089).  The sequence “G-T-G-T-G-T-C-A-C-A-C-A” contains four different nucleotides (A, C, T, and G). Furthermore, this sequence contains three nucleotides before a fourth nucleotide (G,T, and C occur before A), where each of G and T occur at least twice before A.  GenBank AC133089 teaches that this sequence occurs consecutively in M. musculus (page 1).  This sequence contains an equal number of A, C, T, and G nucleotides (three of each).  The sequence “G-T-G-T-G-T-C-A-C-A-C-A-G-T-G-T-G-T-C-A-C-A-C-A” taught by GenBank AC133089 therefore reads on the flow ordering recited in claim 21 (page 1).
Regarding claims 37 and 39, the sequence “G-T-G-T-G-T-C-A-C-A-C-A” contains two different nucleotide species which occur three times before the fourth nucleotide species (both G and T occur three times before A).
Furthermore, with regards to sequencing chromosome 19 of M. musculus, Grimwood is a research article that teaches sequencing of chromosome 19 in humans and mice (Title, Abstract, see the entire document for instance, Figure 2).  Grimwood teaches that chromosome 19 is of particular interest for sequencing and can be important in comparative genomic analyses of gene orthology in rodents and humans (Abstract, Figure 2).  Grimwood further teaches that chromosome 19 in humans and mice is a chromosome rich in biological and evolutionary significance (Abstract and Figure 2).  Furthermore, it is known in the art that M. musculus (i.e., mouse) is an important model organism for studying, among other things, human diseases and evolutionary conservation (Abstract, and page 531, left column, second paragraph).  Thus, a practitioner would be motivated to sequence the genome of a mouse, including chromosome 19 as taught by GenBank AC133089/Grimwood.
It would have been obvious to one of ordinary skill in the art at the time the invention was made to modify Rothberg’s pyrosequencing method by delivering nucleotides according to a predetermined ordering of Garcia because it would have merely required combining known elements according to known methods to yield predictable results. One would have been motivated to combine Rothberg and Garcia to properly and accurately sequence the p53 gene taught by Garcia, which has been associated with cancer, as taught by Garcia. It would have been predictable to do so because Rothberg teaches that the apparatus is intended to be used for sequencing-by-synthesis applications ([0124]) and further teaches that the nucleotides may be delivered in any order ([0334]).  Furthermore, Garcia teaches the additional motivation of using their pre-programmed/predetermined nucleotide dispensation flow sequence when sequencing in general because such a method improves the speed and read length of sequencing, and also corrects out-of-phase problems (Abstract).  Therefore, the advantages of the sequencing method of Garcia can be broadly applied to sequencing of any organism.  As such, a practitioner would be further motivated to use the sequencing method of Garcia to sequence the M. musculus genome including chromosome 19, as taught by GenBank AC133089 and Grimwood, as mice are known to be important model organisms for human and evolutionary studies (Grimwood, Abstract, Figure 2, page 531).  A practitioner would therefore flow the sequence “G-T-G-T-G-T-C-A-C-A-C-A-G-T-G-T-G-T-C-A-C-A-C-A” when sequencing chromosome 19 of  M. musculus using the sequencing method suggested by the teachings of Rothberg/Garcia, where this sequence and resulting flow ordering reads on the flow ordering limitations of claims 21, 37, and 39.
Response to Arguments
Applicant's arguments filed 2/21/2024 have been fully considered but they are not persuasive. The Applicant argues that the sequence presented in the office action mailed 11/21/2023 does not necessarily represent a flow ordering but does not offer a further argument to this point.  The rationale presented in the non-final office action mailed 11/21/2023, where a sequence that a practitioner would reasonably sequence using the methods of Rothberg/Garcia represents a flow ordering, has therefore not been refuted.
The Applicant argues that their amendments are sufficient to overcome the original rejection.  This argument is persuasive.  However, the Applicant’s amendments prompted a new search, and the limitations of the presently recited flow orderings in claims 21-39 read on sequences which were known at the time of filing, and further these sequences could reasonably have been sequenced by a motivated practitioner at the time of filing using the methods of Rothberg/Garcia.  The newly recited flow orderings are therefore rendered obvious by the prior art (see new 103 rejections, above).
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA  as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/process/file/efs/guidance/eTD-info-I.jsp.
Claims 21-39 are rejected on the ground of non-statutory double patenting as being unpatentable over claims 1-17 of U.S. Patent No. 9,605,308.
The patented claims teach an apparatus for sequencing a polynucleotide strand comprising a flow chamber for receiving flows of different dNTP reagents, multiple reservoirs that contain a different dNTP, flow paths from each of the reservoirs to the flow chamber, and a fluidics controller that is programmed to successively provide flow from the multiple reservoirs to the flow chamber according to an alternate ordering (see patented claim 1). The patented claims teach that the alternate ordering comprises the same number of flows for each of four different dNTP reagent flows and comprises a flow of nucleotides N-W-N-Z and is successively repeated at least once (see patented claim 1). The patent’s specification teaches that a preferred nucleotide flow ordering is TACAT-ACGCA-CGTGC-GTATG (column 8, lines 1-5), and also includes claim language in claim 1 indicating that the flow sequence is repeated. The patent’s specification further describes the sequencing instrumentation (see columns 10-12), which further addresses the structural limitations of the current claims. These disclosures of the preferred alternate nucleotide sequence flow ordering and further the preferred structural features of the apparatus indicate that meet the limitations of the current claims indicates that the patented claims and the current claims each encompass overlapping subject matter.
Response to Arguments – Double Patenting
Applicant's arguments filed 11/21/2023 have been fully considered but they are not persuasive. The applicant has not provided an argument explaining why the recited claims are not instances of double patenting.  The non-statutory double patenting rejection is therefore maintained.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action.  Accordingly, THIS ACTION IS MADE FINAL.  See MPEP § 706.07(a).  Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action.  In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action.  In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.

CITED REFERENCE SUMMARIES: Ref US20090127589: Claims:
1. An apparatus, comprising:
an array (100) of CMOS-fabricated sensors (105), each sensor comprising one chemically-sensitive field effect transistor (chemFET) (150) and occupying an area on a surface of the array of approximately ten micrometers by ten micrometers or less.
2-20. (canceled)
21. A sensor array (100), comprising:
a two-dimensional array of electronic sensors (105) including at least 512 rows and at least 512 columns of the electronic sensors, each sensor comprising one chemically-sensitive field effect transistor (chemFET) (150) configured to provide at least one output signal representing a presence and/or concentration of an analyte proximate to a surface of the two-dimensional array.
22-40. (canceled)
41. An apparatus, comprising:
an array (100) of CMOS-fabricated sensors (105), each sensor comprising one chemically-sensitive field effect transistor (chemFET) (150), wherein the array of CMOS-fabricated sensors includes more than 256 sensors, wherein a collection of chemFET output signals from all chemFETs of the array constitutes a frame of data, and wherein the apparatus further comprises: control circuitry (110, 192, 194, 198) coupled to the array and configured to generate at least one array output signal (Vout) to provide multiple frames of data from the array at a frame rate of at least 1 frame per second.
42-50. (canceled)
51. An apparatus, comprising:
an array (100) of CMOS-fabricated sensors (105), each sensor comprising a chemically-sensitive field effect transistor (chemFET) (150), the chemFET comprising:
a floating gate structure (170); and
a source (156) and a drain (158) having a first semiconductor type and fabricated in a region (154) having a second semiconductor type, wherein there is no electrical conductor that electrically connects the region having the second semiconductor type to either the source or the drain.
52-73. (canceled)
74. An apparatus, comprising:
an array (100) of electronic sensors (105), each sensor consisting of three field effect transistors (FETs) including one chemically-sensitive field effect transistor (chemFET) (150).
75. (canceled)
76. An apparatus, comprising:
an array (100) of electronic sensors (105), each sensor comprising three or fewer field effect transistors (FETs), wherein the three or fewer FETs includes one chemically-sensitive field effect transistor (chemFET) (150).
77. An apparatus, comprising:
an array (100) of electronic sensors (105), each sensor comprising:
a plurality of field effect transistors (FETs) including one chemically-sensitive field effect transistor (chemFET) (150); and
a plurality of electrical conductors electrically connected to the plurality of FETs,
wherein the plurality of FETs are arranged such that the plurality of electrical conductors includes no more than four conductors traversing an area occupied by each sensor and interconnecting multiple sensors of the array.
78. An apparatus, comprising:
an array (100) of CMOS-fabricated sensors (105), each sensor comprising a plurality of field effect transistors (FETs) including one chemically-sensitive field effect transistor (chemFET) (150), wherein all of the FETs in each sensor are of a same channel type and implemented in a single semiconductor region of an array substrate.
79. (canceled)
80. A sensor array (100), comprising:
a plurality of electronic sensors (105) arranged in a plurality of rows and a plurality of columns, each sensor comprising one chemically-sensitive field effect transistor (chemFET) (150) configured to provide at least one output signal representing a presence and/or a concentration of an analyte proximate to a surface of the array, wherein for each column of the plurality of columns, the array further comprises: column circuitry (110) configured to provide a constant drain current and a constant drain-to-source voltage to respective chemFETs in the column, the column circuitry including two operational amplifiers and a diode-connected FET arranged in a Kelvin bridge configuration with the respective chemFETs to provide the constant drain-to-source voltage.
81. A sensor array (100), comprising:
a plurality of electronic sensors (105) arranged in a plurality of rows and a plurality of columns, each sensor comprising one chemically-sensitive field effect transistor (chemFET) (150) configured to provide at least one output signal representing a concentration of ions in an analyte proximate to a surface of the array; at least one row select shift register (192) to enable respective rows of the plurality of rows; and at least one column select shift register (194) to acquire chemFET output signals from respective columns of the plurality of columns.
82-85. (canceled)
86. An apparatus, comprising:
an array (100) of CMOS-fabricated sensors (105), each sensor comprising a chemically-sensitive field effect transistor (chemFET) (150), the chemFET comprising:
a floating gate structure (170); and
a source (156) and a drain (158) having a first semiconductor type and fabricated in a region (154) having a second semiconductor type, wherein there is no electrical conductor that electrically connects the region having the second semiconductor type to either the source or the drain,
 wherein: the array includes a two-dimensional array of at least 512 rows and at least 512 columns of the CMOS-fabricated sensors; each sensor consists of three field effect transistors (FETs) including the chemFET; each sensor includes a plurality of electrical conductors electrically connected to the three FETs; the three FETs are arranged such that the plurality of electrical conductors includes no more than four conductors traversing an area occupied by each sensor and interconnecting multiple sensors of the array; all of the FETs in each sensor are of a same channel type and implemented in a single semiconductor region of an array substrate; and a collection of chemFET output signals from all chemFETs of the array constitutes a frame of data, and wherein the apparatus further comprises: control circuitry (110, 192, 194, 198) coupled to the array and configured to generate at least one array output signal (Vout) to provide multiple frames of data from the array at a frame rate of at least 20 frames per second.
87. A method for processing an array (100) of CMOS-fabricated sensors (105), each sensor comprising a chemically-sensitive field effect transistor (chemFET) (150), the method comprising:
A) dicing a semiconductor wafer including the array to form at least one diced portion including the array; and B) performing a forming gas anneal on the at least one diced portion.
88-93. (canceled)
94. A method for processing an array (100) of CMOS-fabricated sensors (105), each sensor comprising a chemically-sensitive field effect transistor (chemFET) (150) having a chemically-sensitive passivation layer of silicon nitride and/or silicon oxynitride deposited via plasma enhanced chemical vapor deposition (PECVD), the method comprising:
A) depositing at least one additional passivation material on the chemically-sensitive passivation layer so as to reduce a porosity and/or increase a density of the passivation layer.
95-101. (canceled)
102. An apparatus comprising
a chemical-sensitive field effect transistor (chemFET) having disposed on its surface a PPi receptor.
103. A fluidics assembly for use with an array of sensors on an active semiconductor device capped with a protective layer, comprising:
a first member having therein an aperture for mating to the sensor array; and a second member fixed to the first member in a fluid-tight seal therebetween, and having first and second fluid ports for supporting fluid passage, the first and second members and the sensor array defining a fluid chamber, whereby fluid introduced into one of said ports flows over the array before exiting via the other of said ports.
104. A fluidics assembly for use with an array of sensors on an active semiconductor device capped with a protective layer, comprising:
a microwell array configured and arranged to provide fluid access to said protective layer; a first member having therein an aperture for mating to the sensor array around the microwell array; and a second member fixed to the first member in a fluid-tight seal therebetween, and having first and second fluid ports for supporting fluid passage, the first and second members and the microwell array defining a fluid chamber over the protective layer of the semiconductor device when mated to the sensor array, whereby fluid introduced into one of said ports flows over the microwell array before exiting via the other of said ports and the active semiconductor device senses chemical activity in at least some of the microwells in the microwell array.
105-106. (canceled)
Ref US9605308: Claims:
1. An apparatus for sequencing a polynucleotide strand, comprising:
a flow chamber for receiving flows of different dNTP reagents;
multiple reservoirs that each contain a different dNTP reagent;
flow paths from each of the reservoirs to the flow chamber; and
a fluidics controller that controls the flow from the reservoirs to the flow chamber, wherein the fluidics controller is programmed to successively provide flow from the multiple reservoirs to the flow chamber according to a predetermined ordering, wherein the predetermined ordering comprises an alternate ordering which is not a continuous and ordered repeat of four different dNTP reagent flows, the alternate ordering comprising a same number of flows for each of four different dNTP reagent flows, a flow of a nucleotide N, which is followed directly by a flow of a different nucleotide W, which is followed directly by a flow of the same nucleotide N, wherein the N-W-N flow is further followed directly by a flow of a nucleotide Z that is different from N and W, and the alternate ordering being successively repeated at least once.
2. The apparatus of claim 1, wherein the alternate ordering is not a continuous repeat of an order of a first four dNTP reagent flows in the predetermined ordering.
3. The apparatus of claim 1, further comprising a flow cell loaded into the flow chamber, wherein the flow cell comprises a microwell array that contains multiple copies of the polynucleotide strand with a primer annealed thereto.
4. The apparatus of claim 3, wherein the flow cell further comprises a chemFET sensor array for detecting the reaction of the dNTP reagent with the contents of the microwell array.
5. The apparatus of claim 3, wherein the polynucleotide strands are attached to beads that are contained in the microwells of the microwell array.
6. The apparatus of claim 1, wherein the predetermined ordering consists of only the alternate ordering.
7. The apparatus of claim 1, wherein the predetermined ordering further comprises a continuous and ordered flow of the four different dNTP reagent flows as follows: dATP, then dCTP, then dGTP, and then dTTP.
8. The apparatus of claim 1, wherein a first four dNTP reagent flows of the continuous and ordered repeat of the four different reagent flows comprises: dATP, then dCTP, then dGTP, and then dTTP.
9. The apparatus of claim 1, wherein the predetermined ordering includes a first portion that comprises the alternate ordering and a second portion that does not comprise the alternate ordering.
10. The apparatus of claim 1, wherein in the predetermined ordering, the flow of one of the four dNTP reagent flows is always followed by a flow of a different one of the four dNTP reagent flows.
11. The apparatus of claim 1, wherein the predetermined ordering further comprises a continuous and ordered repeat of the four different dNTP reagent flows and is a permutation of a flow ordering of: dATP, then dCTP, then dGTP, and then dTTP.
12. The apparatus of claim 1, wherein the alternate ordering is repeated two or more times.
13. An apparatus for sequencing a polynucleotide strand, comprising:
a flow chamber for receiving flows of different dNTP reagents;
multiple reservoirs that each contain a different dNTP reagent;
flow paths from each of the reservoirs to the flow chamber; and
a fluidics controller that controls the flow from the reservoirs to the flow chamber, wherein the fluidics controller is programmed to successively provide flow from the multiple reservoirs to the flow chamber according to a predetermined ordering, wherein the predetermined ordering comprises an alternate ordering which is not a continuous and ordered repeat of four different dNTP reagent flows, the alternate ordering comprising a flow of one kind of dNTP reagent always followed by a flow of a different kind of dNTP reagent, at least one flow of each kind of dNTP reagent followed by a flow of the same kind of dNTP reagent after a single intervening flow of a different kind of dNTP reagent, a same number of flows of each of the four kinds of dNTP reagent flows in the alternate ordering, and wherein repetition of the alternate ordering successively occurs at least once to sequence a desired template length.
14. The apparatus of claim 13, wherein the alternate ordering is repeated two or more times.
15. The apparatus of claim 1, wherein the plurality of reagent flows in the alternate ordering comprises one of 8, 12, 16, 20, 24, 28 and 32 dNTP reagent flows.
16. The apparatus of claim 13, wherein the plurality of reagent flows in the alternate ordering comprises one of 8, 12, 16, 20, 24, 28 and 32 dNTP reagent flows.
17. An apparatus for sequencing a polynucleotide strand, comprising:
a flow chamber for receiving flows of different dNTP reagents;
multiple reservoirs that each contain a different dNTP reagent;
flow paths from each of the reservoirs to the flow chamber; and
a fluidics controller that controls the flow from the reservoirs to the flow chamber, wherein the fluidics controller is programmed to successively provide flow from the multiple reservoirs to the flow chamber according to a predetermined ordering, wherein the predetermined ordering consists of only an alternate ordering which is not a continuous and ordered repeat of four different dNTP reagent flows, the alternate ordering comprising a same number of flows for each of four different dNTP reagent flows, a flow of a nucleotide N, which is followed directly by a flow of a different nucleotide W, which is followed directly by a flow of the same nucleotide N, wherein the N-W-N flow is further followed directly by a flow of a nucleotide Z that is different from N and W, and the alternate ordering being repeated at least once.