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 .
Notice of New Examiner
This case has been transferred to a new examiner for continued examination. Any further communications regarding this case may be directed to the contact information included in the conclusion of this office action.
Status of Claims
Applicant's amendment filed 02/03/2026 is acknowledged. Claim 27 has been amended. Claims 37-39 have been added. Claims 1-26 are cancelled. Claims 27-39 are pending in the instant application and the subject of this non-final office action.
All of the amendments and arguments have been reviewed and considered. Any rejections or objections not reiterated herein have been withdrawn in light of amendments to the claims or as discussed in this office action.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Previous Rejection
Status of Prior Rejections/Objections:
The 112(b) rejections to claim(s) 27-36 is/are withdrawn in view of the amendments to claim 27. See new 112(b) rejections.
The previous prior art and the non-statutory double patenting rejections are each withdrawn. See new 103 and double patenting rejections.
New Ground(s) of Rejections
The new ground(s) of rejections were necessitated by applicant’s amendment of the claims.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim Objections
Claim 27, 34, and 39 are objected to because of the following informalities:
Claims 27 and 39, in (b), recite “sub- set”. This should read “sub-set” without the space.
Claims 27 recites, in (b) and (e), “sub-set”. Claim 34 recites “each of the subsets”. Applicant is required to choose one format for consistency.
Appropriate correction is required.
Specification (Nucleotide and/or Amino Acid Sequence Disclosures)
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is missing or incomplete. See item 1) a) or 1) b) above.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Claim Rejections - 35 USC § 112(b)
Claim 27-39 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding claims 27 and 39, the claims recite “labels that are associated with the sample in (b)” in (d). The claim previously recites “labeling the sample with a plurality of capture agents” in (a) and “hybridizing a first subs- set of a plurality of labeled nucleic acid probes with the sample” in (b).
It is not clear whether the “labels that are associated with the sample in (b)” is intended to include both the labels recited in (a) and (b), only those of (b), or some other label (e.g., unrecited labels that may be applied in step (b) and considered broadly “associated” by being in the neighborhood but not specifically hybridized). This is an antecedent basis rejection.
Claims 28-38 are indefinite for depending from claim 27 and not rectifying the deficiency.
Regarding claims 35 and 36, the claims recite “the probes”. Claim 27 recites, in (b) “a first sub- set of a plurality of labeled nucleic acid probes” and that in (e) step (b) is repeated with “a different sub-set” of the plurality of the labeled nucleic acid probes”.
It is not clear whether “the probes” refers to “the first sub-set” in the first repetition, all subsets across all repetitions, or something else.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 35 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Regarding claims 35, the amended claim 27 recites “inactivating or removing the labels that are associated with the sample in (b), wherein removing the labels comprises exposing the sample to a chemical denaturant”. Claim 35 recites “the probes are removed in step (d) by denaturation”.
The removal is now required to be with a chemical denaturant in claim 27. Claim 35 broadens this removal by reciting “by denaturation” which may encompass other types of denaturation.
Thus, the claims fail to comply with the requirements of 112(d).
Claim Rejections - 35 USC § 103
Claim(s) 27-35 and 37-39 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gao (US 2015/0004598 A1; effectively filed 04/25/2011; as cited in the IDS dated 10/11/2021) in view of Kochar (US 2020/0105409 A1; effectively filed 07/23/2015).
Regarding claims 27 and 35, Gao teaches a method of sample analysis (entire document, e.g., para [0009-44], [0083-84], [0179], [294-0412]; Fig. 1; claim 30-35) comprising:
labeling the sample with a plurality of capture agents (Fig. 1; para [0295]);
specifically hybridizing a first sub-set of a plurality of labeled nucleic acid probes with the sample (Fig. 1; para [0296]);
reading the sample to obtain an image showing binding pattern for each of the probes hybridized in step (b) (Fig. 1; para [0297]);
inactivating or removing the labels that are associated with the sample in (b), wherein removing the labels comprises exposing the sample to a chemical denaturant (para [0299]; [306]: “100. … removing”; [0307]: “101. The method or …100, wherein the quenching is chemical”; [0308]: “The method of … 101, wherein said [chemical] quenching is … denaturation”; instant claim 35; see also “inactivating” in para [0306-308]: e.g., “photo-bleaching”);
repeating steps (b) and (c) multiple times with a different sub-set of the plurality of the labeled nucleic acid probes, each repeat followed by step (d) except for the final repeat (para [0300-302], where the last repeated steps l and m are contacting with nucleic acid probes and detecting; see also para [0148] and [0043] regarding multiple times)
Regarding claim 28, Gao teaches providing solid supports bearing affinity molecules, which may comprise samples, wherein the solid supports may be a well (para [0013]).
Regarding claim 31, Gao teaches the contact time between the sample and the single-stranded nucleic acid can be at least about 1 minute or at least about 5 minutes and that the artisan would adjust the contact time and conditions (para [0173]).
Regarding claim 32, Gao teaches the erasing and relabeling steps can be cycled or repeated as many times as needed to detect the desired number of analytes in the sample, including 2-20 times (para [0148]).
Regarding claim 33, Gao teaches that a plurality can comprise 10 or more different members (para [0140]) such that a plurality of capture agents would be understood to comprise 10 or more (claim 30a).
Regarding claim 34, Gao teaches that the number of analytes identified in each cycle can be 2-4 (para [0148]), i.e., that the subset of corresponding probes specifically hybridized would be 2-4. See also the teachings of spectral unmixing (e.g., para [0178]) and multispectral (comprising two discrete wavelengths)/hyperspectral imagine (para [0176-177]).
Gao teaches utilization of semi-automated cyclic staining and real-time monitoring of staining and de-staining (para [0426]). Gao integrates by reference various systems for multispectral/hyperspectral imaging (para [0176-177]).
Gao teaches label moiety may selected from a variety of moieties in at least para [0328].
Gao fails to explicitly teach:
a system for analyzing a sample comprising a processor, computer-readable memory comprising instructions, and a controller capable of the analysis of the method (claim 27);
an auto-sampler (claim 29), wherein the autosampler is configured to label the sample with the plurality of capture agents (claim 30);
that the controller is configured to operate pump(s) configured to deliver reagent(s) (claim 37), wherein that reagent may comprise an oligonucleotide mix, a wash solution, and/or a chemical denaturant (claim 38).
Kochar teaches an automated assay system for conducting biological assays including immunoassays (entire document, e.g., para [0006]) and nucleic acid hybridization assays (para [0205]). Kochar teaches that the test sites may be wells (para [0321]; see also para [0414-430] and, e.g., para [0127]: “analyzing a plurality of samples in 96-well plates”). Kochar teaches that detection may be a variety of detection means in para [0206]).
Kochar teaches a computer readable medium having stored thereon a computer program which, when executed by a computer system operatively connected to an assay system, causes the assay system to perform a method of conducting an assay on said assay system, wherein said assay system further comprises a processor (para [0014-17]), wherein the method comprises conducting said assay system using said assay consumable (para [0018-23]) (instant claim 27 and 39). Kochar teaches a control instructs the assay system to conduct an assay (para [0356]).
Kochar teaches that the assay system may comprise a robotic controlled pipettor
and a robotic controlled gripper arm, an assay reader, a plate washer, and at least one processor adapted to execute at least one instruction to minimize potential errors
in loading of the consumables and in running the assay (para [0074]).
Kochar teaches that the robotically controlled pipettor of the system is capable of automatically dispensing samples [i.e., is auto-sampler] (Fig. 12M-a; instant claim 29) and is configured to label samples with capture agents [e.g., antibodies] (Fig. 13f, Fig. 14d); instant claim 30). Kochar teaches that embodiments of the system may comprise subsystems with individual robotic subsystems configured to access and move or more consumables from one subsystem to another, comprising a pipetting subassembly, a plate washing subassembly, and the assay reader (para [0223]).
Kochar teaches that the pipetting subassembly includes appropriate pumps for controlling the pipettors and driving fluids [including reagents, see earlier in para [0228]) through the pipetting subassembly (para [0228], [0245]; see also para [0245]; instant claim 37).
Kochar teaches biological reagents that may be used in such system include nucleic acids and oligonucleotides (para [0205]) and other binding reagents, wash solutions, and sample processing reagents (para [0320]; instant claim 38).
Kochar teaches the software architecture enables the ability to customize protocols to a particular assay (para [0008]). Kochar teaches tailoring one or more steps of an assay to an individual consumable/lot of consumables (para [0353]), including the sequence of steps to be applied by the reader during the assay (para [0355]).
Kochar teaches that repeatability and reproducibility remain goals for all automated assay systems (para [0005]). Kochar teaches that its automated system is capable of performing such assay runs with reproducible results and probably human or machine errors that may occur in the preparation for an assay run and during an assay run have been identified and minimized (para [0006]).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have programmed the method of Gao on to the automated assay system of Kochar comprising a processor and computer readable medium and a controller that executes said program for analysis (claim 27 and 39), the robotically controlled pipettor/auto-sampler configured to label a sample with capture agents (claims 29-30), and a controlled pump configured to deliver at least oligonucleotides and was solution (claims 37-38), motivated by the desire to minimize human errors in the performance of the assay, as suggested by Kochar, and because automating manual activities is obvious as discussed in MPEP 2144.04(III).
Additionally, while about 1 minute may be interpreted to be about 2 minutes (claim 31), the hybridization time also represents a results effective variable that would be obvious to the POSITA before the EFD to adjust at least because Gao teaches a range and that such is adjusted by the artisan, wherein such adjustments would therefore be predictable.
Where the embodiments of Gao may be directed to other means of erasing/quenching, it would have been obvious to the POSITA before the EFA of the claimed invention to have substituted the means of quenching/removal of the chemical denaturant, as discussed in MPEP 2144.06, as selecting chemical denaturants in Gao are taught as suitable means for quenching.
Where embodiments of Gao may be interpreted to not teach repetition, such would have been obvious to the POSITA before the EFD of the claimed invention as Gao elsewhere teaches repeating steps of its methods for the cited number of times and such represents no more than the duplication of “parts”, as discussed in MPEP 2144.04(VI)(B), wherein the number of repetitions further represents a results effective variable at least because of the range of values provided by Gao.
There would have been a strong expectation for success as both are directed to overlapping detection means, Gao teaches that a semi-automated method had already been performed and contemplates use of systems for imaging, and Kochar contemplates use of such a system with both oligonucleotides and antibodies. Such represents the application known device/technique to a known method for predictable improvement.
It is noted that while claims 27 and 39 have different scopes, repeating claim 27 at least 2 times encompasses claim 39, as it recites “comprises”, wherein the second (b) and (c) may follow the one pass as unrecited steps.
Claim(s) 36 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gao (US 2015/0004598 A1; effectively filed 04/25/2011; as cited in the IDS dated 10/11/2021) in view of Kochar (US 2020/0105409 A1; effectively filed 07/23/2015) applied to claims 27-35 and 37-39 above, and further in view of Sussman (US 2016/0346330; filed 11/12/2015).
Regarding claim 36, Gao teaches washing with a suitable wash buffer at a temperature greater than the melting temperature of the hybridized nucleic acid strands to remove the label (para [0182]) and using such in the method (para [0308]: “washing”). As cited above in claim 27, Gao teaches that the label may be removed by a chemical denaturant.
Gao teaches that its assay may be considered a FISH (para [0014])
Gao fails to explicitly teach that the chemical denaturant may be 70-90% formamide and applying it for a period of at least 1 minutes followed by a wash.
Sussman teaches denaturing DNA in the context of a fluorescent in situ hybridization [i.e., FISH], by immersing samples in 70% formamide for 2 minutes and following with at least one wash (para [0121]). Sussman also teaches performing with an alternative percentage of formamide at a different amount of time, also followed by at least one wash (para [0121]).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized formamide at 70% as the chemical denaturant of Gao in the combined system, as such was known to be suitable for the same purpose as discussed in MPEP 2144.07 or as an obvious species of the genus of chemical denaturants. In having chosen the formamide of Sussman, it would be obvious to the POSITA before the EFD of the claimed invention to have followed the steps of applying for 2 minutes and following with at least one wash, motivated by the desire to achieve the predictable outcomes of Sussman for the FISH assay. Such would be obvious as Gao teaches combining with at least one wash, wherein the order of steps is obvious absent unexpected results, as discussed in MPEP 2144.04(IV)(C). The timing and percentage are also determined to be results effective variables as Sussman teaches at least two versions, wherein such differ by the application timing (and iterations) and wash procedures, as further discussed in MPEP 2144.05.
There would have been a strong expectation of success as Gao teaches chemical denaturants and washes and is directed to FISH such that the substitution and optimizations of Sussman would be expected to perform their expected functions to achieve their expected results when combined for their commonly known purpose.
Double Patenting
Claims 27-39 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 of U.S. Patent No. 10,370,698 B2 in view of Kochar (US 2020/0105409 A1; effectively filed 07/23/2015).
Both sets of claims are directed to analyzing a sample comprising labeling a sample with a plurality of capture agents; specifically hybridizing a first subset of labeled nucleic acid probes with the sample; reading the sample to obtain a binding pattern for each of the probes hybridized in the previous step; removing the probes hybridized by denaturation by incubating the sample in 70%-90% of formamide; and repeating the specific hybridization, reading to obtain an image, and removal except for the final repetition where the probes are not removed.
‘698 recites the repeating is 2-20 times (claim 13; instant claim 32); there are at least 10 capture agents (claim 10; instant claim 33); the subset is independently 2-4 labeled NA probes (claim 11; instant claim 35); the 70-90% formamide is applied for 1 min followed by a wash (claim 12; instant claim 36);
‘698 fails to explicitly teach:
a system for analyzing a sample comprising a processor, computer-readable memory comprising instructions, and a controller capable of the analysis of the method (claim 27);
the sample is in a sample well (claim 28);
the system comprises an auto-sampler (claim 29) configured to label the sample with the capture agents (claim 30); and
the system controller is configured to operate pump(s) configured to deliver reagent (claim 37) and the identity of the configured reagent (claim 38).
As discussed and cited in the 103 above, Kochar teaches:
a system for analyzing a sample comprising a processor, computer-readable memory comprising instructions, and a controller capable of the analysis of the method (claim 27);
the system comprises an auto-sampler (claim 29) configured to label the sample with the capture agents (claim 30); and
the system controller is configured to operate pump(s) configured to deliver reagent (claim 37) and the identity of the configured reagent (claim 38).
Kochar teaches the software architecture enables the ability to customize protocols to a particular assay (para [0008]). Kochar teaches tailoring one or more steps of an assay to an individual consumable/lot of consumables (para [0353]), including the sequence of steps to be applied by the reader during the assay (para [0355]).
Kochar teaches that repeatability and reproducibility remain goals for all automated assay systems (para [0005]). Kochar teaches that its automated system is capable of performing such assay runs with reproducible results and probably human or machine errors that may occur in the preparation for an assay run and during an assay run have been identified and minimized (para [0006]).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have programmed the method of ‘698 on to the automated assay system of Kochar comprising a processor and computer readable medium and a controller that executes said program for analysis (claim 27 and 39), the robotically controlled pipettor/auto-sampler configured to label a sample with capture agents (claims 29-30), and a controlled pump configured to deliver at least oligonucleotides and was solution (claims 37-38), motivated by the desire to minimize human errors in the performance of the assay, as suggested by Kochar, and because automating manual activities is obvious as discussed in MPEP 2144.04(III).
There would have been a strong expectation for success as Kochar contemplates use of such a system with both oligonucleotides and antibodies and discusses means of reducing errors, wherein such a modification represents the application known device/technique to a known method for predictable improvement.
Response to Arguments
Applicant's arguments filed 02/03/2026 have been fully considered but they are not persuasive.
Applicant arguments directed to Cai, Huang, Janse, and Karger are moot as the art has not been applied herein.
Regarding the arguments directed to Cai, Applicant argues on pgs. 6-7 that Gao does not teach or suggest inactivating label associated with a sample. Applicant alleges that contrary to this, Gao teaches the de-staining of a sample is challenging and unpredictable but teaches effective method for removing the stains/labels via DNA link displacement, citing [0430] and [0436]). Applicant argues that the artisan would have adopted this approach of Gao and would not have had a reasonable expectation of success in achieving the inactivation of labels for a chemical denaturant as presently claimed. Applicant further argues that Sussman fails to cure the deficiencies of the previously applied combination so the artisan would not have attempted to modify Gao to include inactivation of labels or removal of labels by exposing to a chemical denaturant and thus would have no reason to look to Sussman for specific denaturants.
As cited in the current 103 rejection, Gao teaches methods that recite chemical denaturants. Therefore, while Gao also teaches additional embodiments, the artisan would not find the use of chemical denaturants to be unpredictable. As discussed in MPEP 2143.01(I), a suggestion of the claimed invention is not necessarily negated by desirable alternatives. The court stated that "the prior art’s mere disclosure of more than one alternative does not constitute a teaching away from any of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage the solution claimed.
In the instant case Gao explicitly teaches use in its methods and merely recites that DNA link displacement can provide faster de-staining under non-degrading conditions (para [0430]) and that complete or nearly complete specimen de-staining can be achieved solely by introduction of displacement DNA probes under physiological conditions (para [0436]). Such is not interpreted to be a teaching away, particularly view of the additional experiments of Gao and the embodiments cited in in the 103 above that include explicit teaching of chemical denaturation with or without other means of removing labels. See, for example, the low-pH degradation variability experiment that notes that variability may be assigned that the natural variability of biomarker expression and shows good preservation of antigenicity for at least 10 staining cycles (para [0043]).
As such, the artisan also would have had reason to look to Sussman for the reasons described in the 103 above for another suitable chemical denaturant known in the art and corresponding protocol for use thereof.
Regarding the double patenting rejection, on pg. 7, Applicant request that the rejection be deferred until the claims are found allowable as the rejection may become moot if the claims are subsequently amended or cancelled during prosecution.
The Office is unable to hold double patenting rejections in abeyance. The double patenting rejection has been applied in view of Kochar.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Emma R Hoppe whose telephone number is (703)756-5550. The examiner can normally be reached Mon - Fri 11:00 am - 7:00 pm.
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/EMMA R HOPPE/Examiner, Art Unit 1683
/NANCY J LEITH/Primary Examiner, Art Unit 1636
Prosecution Insights