DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Herein, “the previous Office action” refers to the Non-Final Rejection filed on 7/17/2025.
Amendments Received
Amendments to the claims were received on 10/17/2025.
Priority
As detailed on the Filing Receipt filed 11/30/2021, the instant application claims priority to as early as 9/16/2020. At this point in prosecution, all claims are accorded the earliest claimed priority date.
Information Disclosure Statement
The Information Disclosure Statement filed on 10/17/2025 is compliance with the provisions of 37 CFR 1.97 and have been considered in full. A signed copy of the IDS is included with this Office Action.
Claim Status
Claims 2, 9-10, 12, 14, 17, 19, 22, 24, 26, 33, 35 and 38-40 are canceled.
Claims 1, 3-8, 11, 13, 15-16, 18, 20-21, 23, 25, 27-32, 34, 36-37 and 41-45 are pending.
Withdrawn Objections/Rejections
The objection to claim 32 is withdrawn in view of Applicant’s amendment.
The rejection of claim 16 under 35 USC § 112(b) is withdrawn in view of Applicant’s amendment of the claim to remove relative terminology (“substantially”).
The rejection of claim 36 under 35 USC § 112(b) is withdrawn in view of Applicant’s amendment of the claim introducing the terminology "to minimize...," which is supported in the specification at [163] including a definition there of "optical crowding" and its relationship to "minimizing" disclosed there.
The rejections of claim 2 under 35 USC §§ 101 and 103 are withdrawn in view of Applicant’s cancelation of the claim.
Claim Objections
Claim 45 is objected to because of the following informalities:
The recited “to obtaining… detecting… determining… correcting… and detecting” (lines 5, 7, 12, 17 and 24) should be amended for grammatical consistency, to read either “to perform a method comprising obtaining… detecting… determining… correcting… and detecting” or “to obtain… detect… determine… correct… and detect”. Also, a colon should follow "...processors to..."
Appropriate correction is required.
Response to Arguments - Claim Rejections Under 35 USC § 101
In the Remarks filed 10/17/2025, Applicant traverses the rejection under 35 USC § 101 and presents supportive arguments.
Applicant alleges at Step 2A, Prong One that the present claims recite steps beyond what can be performed in a human mind and highlights the implemented functions of obtaining sample images, detecting signals therein, and determining oligonucleotide sequences based on the detected signals (Remarks at pg. 10, para. 5 – pg. 11, para. 2).
The Office does not claim that the referenced step of obtaining images can be performed in the human mind. The rejection identifies this step as an additional element that gathers data necessary for performance of subsequent steps encompassing judicial exceptions. Necessary data gathering is considered insignificant extra-solution activity, which is insufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
The § 101 rejection also includes citation to an article authored by Asp et al (BioEssays 42(10): article no. 1900221; published 5/4/2020; previously cited), which reviews spatial transcriptomic approaches including Multiplexed Error Robust Florescence In Situ Hybridization (MERFISH). As described by Asp, MERFISH involves hybridization of probe sequences to target transcripts, imaging on technologies such as spatial and bead arrays, and computational error-correction of resulting sequence reads (Asp at pg. 7; pg. 10, r. column – pg. 12, l. column). As a review article, Asp provides evidence that at least the claimed process of obtaining images, wherein images include locations of barcode probe molecules attached to features of a spatial or bead array, comprises well-understood, routine and conventional activity in the field of the invention. Insignificant extra-solution activity that is well-understood, routine and conventional in the field of the invention is insufficient to provide an inventive concept (MPEP 2106.05(d)).
The referenced step of obtaining images, although not itself directed to a mental process, therefore cannot serve to integrate any recited judicial exceptions into a practical application or provide an inventive concept sufficient to render the claims as significantly more.
The human mind is capable of detecting signals corresponding to barcode probe sequences at locations in an image, and further determining sequence information according to the detected signals. For example, given a scheme wherein a particular colored fluorophore is known to correspond to a particular barcode probe sequence bound to a particular target sequence, the human mind is capable of detecting the presence of the particular barcode probe sequence at image locations that display the corresponding color and further determining that the particular target sequence is present at said image locations.
Hence, the referenced steps of detecting signals and determining sequences are considered to encompass mental processes under their broadest reasonable interpretation, and the argument against direction to mental processes is found unpersuasive.
Applicant asserts at Step 2A, Prong One that the present claims do not recite any mathematical equations, and alleges that the claims are therefore not directed to mathematical concepts (pg. 11, para. 2).
Mathematical concepts are not limited to expressly-recited mathematical equations, and further include acts of calculation. Independent claims 1 and 44-45 require calculation of maximum likelihood values based on a probability distribution, while dependent claims 15-16, 18 and 20 further narrow this to iterative calculation of maximum likelihood values based on a probability distribution provided by a neural network or random forest model. The recited acts of calculation, including those utilizing particular algorithms, are viewed as mathematical concepts. Hence, the argument against direction to mathematical concepts is unpersuasive.
Applicant asserts that at Step 2A, Prong Two the instant claims detect "target analytes" and so are "directed to the practical application of detecting spatial presence (e.g., expression)" (pg. 11, para. last). At Prong Two, the MPEP summarizes "considerations" from case law toward arguing practical application (citations below). More persuasive than directly arguing top level allowability, 101 patent eligibility, or even practical application, is discussion of one or more of the MPEP "considerations" towards establishing practical application. In Applicant's remarks, it is not yet clear that the alleged practical application is, for example, any of the considerations: improvement over the previous state of the technology field (MPEP 2106.04(d) and (d)(1)), administration of a particular treatment for a medical condition (MPEP 2106.04(d) and (d)(2)) or transformation of a particular article (MPEP 2106.04(d) and 2106.05(c)). In Applicant's remarks, a conclusion of "practical application" is asserted regarding "detecting...," but without yet providing persuasive, supporting explanation. It may help to further discuss one or more of the MPEP considerations.
Applicant asserts that, similarly to claims held eligible in BASCOM Global Internet Servs. v. AT&T Mobility LLC, 827 F.3d 1341 (Fed Cir. 2016, hereafter “BASCOM”), the present claims recite specific limitations comprising an ordered, non-conventional combination of elements that provide an inventive concept (pg. 12, para. 2 – pg. 13, para. 1).
The claims considered in BASCOM were directed to a content filtering system and server for filtering content retrieved from an Internet computer network. The court found these claims to recite a particular combination of technical features providing an improvement in the functioning of the claimed computer system over prior content filtering systems, despite conventionality of the claimed elements as considered individually (827 F.3d at 1348-51). The BASCOM court specifically noted that the claims considered therein did not merely recite abstract ideas and require their performance with generic computer components, which would not have conferred eligibility, but were found eligible due to provision of said improvement as supported by the specification (827 F.3d at 1351).
Limitations drawn to the referenced claim features encompass a number of judicial exceptions, and the unconventional nature in combination of these judicial exceptions is not germane to patentability under § 101 (RecogniCorp, LLC v. Nintendo Co., 855 F.3d 1322, 1327-28 (Fed. Cir. 2017)). Recited additional elements beyond said exceptions include the referenced step of obtaining images and the limitation of recited steps to performance by computer hardware.
Obtaining images as claimed is indicated as well-understood, routine and conventional activity in the field of the invention by cited art (Asp et al). Therefore, the addition of this necessary data gathering activity to the recited judicial exceptions does not confer eligibility to the claims.
The instant specification indicates that the claimed computer hardware encompasses generic computer hardware (e.g., “one or more processors coupled directly or indirectly to memory through a system bus”, see specification at paras. 0258-59), and limitation of recited steps to performance by generic computer hardware is insufficient to provide significant inventive concept to the judicial exceptions encompassed therein. Therefore, the addition of this limitation to the recited judicial exceptions does not confer patent eligibility to the claims.
Unlike the claims considered in BASCOM, the present claims merely gather data required for performance of steps directed to judicial exceptions and implement these steps with generic computer hardware. Unlike the specification in BASCOM, neither the instant specification nor the instant record more generally supply sufficient explanation and evidence that technical features of the claimed invention improve the functioning of the claimed computer hardware or the field of the application more generally as compared to technology conventionally employed within the field of the invention. Hence, the argument of analogy to BASCOM is found unpersuasive.
For these reasons, the arguments are found unpersuasive and the rejection is maintained.
Claim Rejections - 35 USC § 101
35 USC § 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1, 3-8, 11, 13, 15-16, 18, 20-21, 23, 25, 27-32, 34, 36-37 and 41-45 are rejected under 35 U.S.C. §101 because the claimed invention is directed to an abstract idea, and a natural phenomenon, without significantly more (i.e., non-statutory subject matter). This rejection is maintained from the previous Office action, and has been revised to address the amended claims (filed 10/17/2025).
"Claims directed to nothing more than abstract ideas, natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 § I).
Abstract ideas include mathematical concepts (including formulas, equations and calculations), and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)).
Laws of nature and natural phenomena include principles, relations, and products that are naturally occurring or do not have markedly different characteristics compared to what occurs in nature (MPEP 2106.04(b)).
The claims as a whole, considering all claim elements both individually and in combination, do not amount to significantly more than an abstract idea and a natural phenomenon.
Step 1: The Four Categories of Statutory Subject Matter (MPEP 2106.03)
Claims 1, 3-8, 11, 13, 15-16, 18, 20-21, 23, 25, 27-32, 34, 36-37 and 41-43 are directed to a method, which falls under the ‘process’ category of statutory subject matter.
Claim 44 is directed to “[a] computing node… [comprising] one or more processors”, which falls under the ‘machine’ category of statutory subject matter.
Claim 45 is directed to “[a] computer program product comprising a computer-readable storage medium”. The claimed subject matter encompasses transitory embodiments (e.g., propagating signals) which do not fall under any category of statutory subject matter. See In re Nuijten, 500 F.3d 1346, 1356-57 (Fed. Cir. 2007); Mentor Graphics Corp. v. EVE-USA, Inc., 851 F.3d 1275, 1294 (Fed. Cir. 2017).
The Examiner suggests amendment to, e.g., “[a] a computer program product comprising a non-transitory computer-readable storage medium”. Direction of the claim to non-transitory embodiments would cause the claim to fall under a category of statutory subject matter and overcome this portion of the rejection.
However, this amendment alone would likely not overcome rejection for recitation of
judicial exceptions without significantly more. In the interest of compact prosecution, the recited subject matter has been interpreted according to the Examiner’s suggestion for further
analysis below regarding recitation of judicial exceptions without significantly more.
Step 2A, Prong One: Whether the Claims Set Forth or Describe a Judicial Exception (MPEP 2106.04 § II.A.1) ‘Mental processes’ are processes that can be performed in the human mind at least with use of a physical aid, e.g., a slide rule or pen and paper (MPEP 2106.04(a)(2) § III). The claims recite elements that encompass processes that are practicably performable in the human mind, at least under their broadest reasonable interpretation, including:
“detecting, in each image, signals at… locations corresponding to… respective barcode probe sequences… [that] are hybridized or bound to… target oligonucleotide sequences or segments thereof in situ” (claims 1 and 44-45), i.e., recognizing spatial information (e.g., colored fluorophore locations) in an image;
“determining… target oligonucleotide sequences based on which decoding cycle and for which locations… [the] respective barcode sequences… are detected” (claims 1 and 44-45), i.e., decoding character strings according to iteration and spatial information;
“correcting… determined target oligonucleotide sequences… to improve an accuracy of the determined… target oligonucleotide sequences, wherein correcting comprises replacement with a known target oligonucleotide sequence, or proxy thereof” (claims 1 and 44-45), i.e., swapping certain derived character strings for known character strings, wherein:
“[the] known target oligonucleotide sequence [is] from a subset of known target oligonucleotide sequences, or proxies thereof, that are within a specified pairwise edit distance of the decoded target oligonucleotide sequence” (claim 11), i.e., decoded and known character strings satisfy a similarity metric threshold,
“the specified pairwise edit distance comprises a specified pairwise Hamming distance of at most two times a specified error correction capability comprising correction of 1, 2, 3, 4, or 5 substitution errors” (claims 13 and 25), i.e., decoded and known character strings satisfy the recited similarity metric threshold;
“detecting the presence of one or more target analytes in a sample based on the one or more corrected target oligonucleotide sequences” (claims 1 and 44-45), i.e., inferring information; and
“each target barcode sequence… is rank-ordered according to an average pairwise edit distance from all other[s]… and assigned to a corresponding target gene transcript of the same rank from a list of corresponding genes rank-ordered by relative expression level” (claim 34), i.e., character strings are organized according to a similarity metric and grouped according to associated information, wherein:
“the rank-ordered unique nucleic acid barcode sequences are assigned to corresponding rank-ordered target gene transcripts such that optical crowding is reduced during a decoding process used to decode the unique nucleic acid barcode sequences” (claim 36).
These recited steps of evaluating and manipulating information, which are practicably performable in the human mind at least with physical aid, constitute mental processes.
‘Mathematical concepts’ are relationships between variables and numbers, numerical formulas or equations, or acts of calculation, which need not be expressed in mathematical symbols (MPEP 2106.04(a)(2) § I). The claims further recite elements which encompass mathematical concepts, at least under their broadest reasonable interpretation, including:
the decoded sequence is replaced by a known oligonucleotide sequence that “has a maximum likelihood as computed from a probability distribution” (claims 1 and 44-45), and is from a subset of known oligonucleotide sequences “wherein the maximum likelihood is computed from the probability distribution for the subset” (claim 11);
“iterative calculation of maximum likelihood for the probability distribution to identify a candidate target oligonucleotide sequence… wherein the probability distribution is updated in each iteration based on the candidate target oligonucleotide sequence barcode” (claim 15), i.e., iteratively re-calculating a probability distribution and maximum likelihood according to character string information, wherein:
“the iterative calculation is complete when: (i) a predetermined number of iterations has been reached, (ii) the probability distribution remains substantially unchanged from one iteration to the next, or (iii) a number of corrected target oligonucleotide sequences remains substantially unchanged from one iteration to the next” (claim 16), i.e., calculation is repeated a predetermined number of times, or until given statistical constraints are satisfied;
“the probability distribution is provided by a probabilistic model comprising a machine learning model” (claim 18); and
“the machine learning model comprises a random forest or neural network model” (claim 20).
The recited acts of calculation, and models, constitute mathematical concepts. Additionally, the recited acts of calculation are (in simple embodiments) practicably performable in the human mind, at least with physical aid, further rendering them as mental processes. For example, the human mind is capable of calculating a maximum likelihood for a given probability distribution wherein the probabilities correspond to incidence of given barcode probe sequences.
Hence, the claims recite elements that, individually and in combination, constitute an abstract idea.
The claims further recite the following claim elements, which require that recited data is
representative of natural phenomena:
the probability distribution “provides probabilities for detecting a given barcode probe sequence at a given location in a given decoding cycle” (claims 1 and 44-45);
“the target oligonucleotide sequences comprise target analyte sequences” (claim 3);
“the target analyte sequences comprise messenger ribonucleic acid (mRNA) sequences” (claim 4);
“the target oligonucleotide sequences comprise target barcode sequences associated with target analytes” (claim 5);
“the target barcode sequences comprise sequences of individual nucleotides” (claim 6);
“the target barcode sequences comprise a plurality of segments, and each segment comprises a plurality of nucleotides” (claim 7);
“the target barcode sequences function as proxies for target analyte sequences” (claim 8);
“a number of decoding cycles in the plurality of decoding cycles is equal to a number of segments in the target oligonucleotide sequences” (claim 21);
“the plurality of target oligonucleotide sequences… comprises a specified total number of unique nucleic acid barcode sequences… [and] each unique nucleic acid barcode sequence, or segment thereof… is selected to have: a specified maximum nucleotide length, a specified minimum pairwise edit distance relative to [the] other unique nucleic acid barcode sequences, or segments thereof… and at least one additional characteristic selected from a list consisting of: a specified total nucleotide length, a specified number of segments, a specified segment length, a specified upper limit on guanine-cytosine (GC) content, a specified maximum length for homopolymer subsequences, and a specified dilution factor for at least one segment” (claim 23), wherein:
“the at least one additional characteristic comprises a specified minimum number of segments of at least two” (claim 27),
“the at least one additional characteristic comprises a specified minimum segment length of at least two nucleotides” (claim 28),
“the at least one additional characteristic comprises a specified upper limit on guanine-cytosine (GC) content of about 50%” (claim 29),
“the at least one additional characteristic comprises a specified maximum length for homopolymer subsequences of 7 nucleotides” (claim 30),
“the at least one additional property comprises a specified decoding dilution factor of at least 10% for the at least one segment” (claim 32), and
“the specified total number of unique nucleic acid barcode sequences is at least 1,000” (claim 37); and
“at least one segment of at least one target barcode sequence of the plurality encodes for an ‘OFF’ state that is not visualized in at least one decoding cycle” (claim 31).
These elements require that data satisfy given representative constraints, but do not alter the abstract nature of the steps performed upon said data. Moreover, these elements specify that data represents particular natural phenomena (e.g., nucleic acid molecules having particular GC content).
The claims must therefore be examined further to determine whether they integrate these judicial exceptions into a practical application (MPEP 2106.04(d)).
Step 2A, Prong Two: Whether the Claims Contain Additional Elements that Integrate the Judicial Exception(s) into a Practical Application (MPEP 2106.04 § II.A.2)
The claims recite the following additional elements directed to data gathering activity necessary for performance of claimed method steps:
“obtaining an image of [a] sample for each decoding cycle of a plurality of decoding cycles to obtain a series of images” (claims 1 and 44-45), wherein:
“the unique nucleic acid barcode sequences… have been incorporated into a set of target-specific probe molecules” (claim 41),
“each unique nucleic acid barcode sequence is attached to a different feature of a spatial array” (claim 42), and
“each unique nucleic acid barcode sequence is attached to a different bead of a bead array” (claim 43).
The claims also require that the user detect, in each image, locations of barcode probe sequences that are hybridized or bound to target oligonucleotide sequences or segments thereof for use in subsequent method steps. This requirement necessitates that the obtained images include locations of barcode probe sequences that are hybridized or bound to target oligonucleotide sequences. Given this requirement, the above limitations (e.g., that analyzed barcodes have been incorporated into probe molecules) are directed to necessary, pre-solutional, data gathering activity.
Insignificant extra-solution activity, including necessary data gathering activity, is insufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g)).
The claims further recite additional elements that require performance of claimed functions on a computer, including:
“A system comprising: a computing node comprising a computer-readable storage medium having program instructions embodied therewith… executable by one or more processors of the computing node to cause the one or more processors to perform” functions of the claimed method (claim 44); and
“A computer program product… comprising a computer-readable storage medium having program instructions embodied therewith, the program instructions executable by one or more processors to” perform functions of the claimed method (claim 45).
The claims do not describe any specific computational steps by which a computer performs or carries out functions drawn to the judicial exceptions, nor do they provide any details of how specific structures of a computer are used to implement these functions. The claims state nothing more than that a generic computer performs functions drawn to the judicial exceptions, and are therefore mere instructions to apply the judicial exceptions using a computer. As such, the claims do not integrate the judicial exceptions into a practical application (see MPEP 2106.04(d) § I and 2106.05(f)).
No further additional elements are recited.
When the claims are considered as a whole: they do not improve the functioning of a computer, other technology, or technical field (MPEP 2106.04(d)(1) and 2106.05(a)); they do not apply the judicial exceptions to effect a particular treatment or prophylaxis for a disease or medical condition (MPEP 2106.04(d)(2)); they do not implement the judicial exceptions with, or in conjunction with, a particular machine (MPEP 2106.05(b)); they do not effect a transformation or reduction of a particular article to a different state or thing (MPEP 2106.05(c)); and they do not apply or use the judicial exceptions in some other meaningful way beyond linking the use of the judicial exceptions to a particular technological environment and/or field of use (e.g., spatial transcriptomics; MPEP 2106.05(e) and 2106.05(h)).
Therefore, the claims do not integrate the judicial exceptions into a practical application. See MPEP 2106.04(d) § I.
Because the claims recite an abstract idea and a natural phenomenon, and do not integrate those judicial exceptions into a practical application, the claims are directed to those judicial exceptions. Claims that are directed to judicial exceptions must be examined further to determine whether the additional elements besides the judicial exceptions render the claims significantly more than the judicial exceptions. Additional elements besides the judicial exceptions may constitute inventive concepts that are sufficient to render the claims significantly more (MPEP 2106.05).
Step 2B: Whether the Claims Contain Additional Elements that Amount to an Inventive Concept (MPEP 2106.05)
As noted above, several recited additional elements amount to insignificant extra-solution activity. Mere addition of insignificant extra-solution activity does not amount to an inventive concept that would render the claims significantly more than the recited judicial exceptions, particularly when the activities are well-understood or conventional (MPEP 2106.05(g)). The conventionality of recited additional elements that amount to insignificant extra-solution activity must be further considered.
Recited additional elements amounting to insignificant extra-solution activity encompass processes which are indicated as well-understood, routine and conventional by relevant prior art. The cited article by Asp et al (BioEssays 42(10): article no. 1900221; published 5/4/2020; previously cited) reviews spatial transcriptomic approaches, including Multiplexed Error Robust Florescence In Situ Hybridization (MERFISH) wherein probe sequences are hybridized to target transcripts, imaged, and resulting sequence reads are computationally error-corrected (pg. 7); and image capturing technologies including spatial and bead arrays (pg. 10, r. column – pg. 12, l. column).
Asp provides evidence that the claimed process of obtaining images, wherein images include locations of barcode probe molecules attached to features of a spatial or bead array probe molecules, comprises well-known, routine and conventional activity in the field of the invention.
Hence, the encompassed extra-solution activity is considered well-understood, routine and conventional. Well-understood, routine and conventional activity is insufficient to constitute an inventive concept that would render the claims significantly more than judicial exceptions (MPEP 2106.05(d)).
Mere instructions to implement judicial exceptions using a computer are, when considered individually, similarly insufficient to constitute an inventive concept that would render the claims significantly more than said judicial exceptions (see MPEP 2106.05(f)).
When the claims are considered as a whole, they do not integrate the judicial exceptions into a practical application; they do not confine the use of the judicial exceptions to a particular technology; they do not solve a problem rooted in or arising from the use of a
particular technology; they do not improve a technology by allowing the technology to
perform a function that it previously was not capable of performing; and they do not
provide any limitations beyond generally linking the use of the judicial exceptions to a particular technological environment and/or field of use (e.g., spatial transcriptomics; MPEP 2106.05(e) and 2106.05(h)).
Therefore, the claims do not provide an inventive concept and/or significantly more than the judicial exceptions themselves. See MPEP 2106.05.
Conclusion: Claims are Directed to Non-statutory Subject Matter
For these reasons, the claims, when the limitations are considered individually and as a whole, are directed to judicial exceptions and lack an inventive concept. Hence, the claimed invention does not constitute significantly more than the judicial exceptions, so the claims are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
Response to Arguments - Claim Rejections Under 35 USC § 103
In the Remarks filed 10/17/2025, Applicant traverses the rejections under 35 USC § 103 and presents supportive arguments pertaining to cited art.
Regarding the rejection of claim 1, Applicant asserts deficiencies in the Office's reliance, first on Press and then on Schober (remarks at pg. 13, para. 4 – pg. 14, para. 1; pg. 14, para. 3).
Contrary to Applicant's assertions, the Office does not rely on Press as teaching a maximum likelihood model to infer a complete target oligonucleotide sequence and instead relies on Schober, as described in the below rejection. And, the Office does not rely on Schober as teaching a corrected barcode to detect a target analyte and instead relies on a combination of Schober (generation of corrected barcodes) and Chen (in situ hybridization). The rejection relies on the combined teachings of Press, Schober and Chen, as further detailed in the rejection.
Applicant asserts that a MiSeq sequencer (the subject of the MiSeq User Guide reference) does not determine the presence and location of target analytes within a sample, i.e., in situ, as claimed (pg. 14, para. 2). The Examiner agrees, as MiSeq User Guide does not specifically discuss analysis of analytes bound in situ.
However, MiSeq User Guide does describe performance of sequencing via imaging of fluorescently-labeled nucleotides bound to sample analytes (pg. 7, pg. 64), and art-of-record Chen discusses performance of the multiplexed error-robust fluorescence in situ hybridization (MERFISH) technique (pg. 1, Abstract) using a MiSeq machine (pg. 11, r. column). In this way, Chen teaches determination of presence and location of target analytes in situ and indicates that the MiSeq platform is compatible with their technique. Hence, the presented distinction between the present claims and the function of a MiSeq machine is found unpersuasive regarding the applied combination of prior art.
Regarding the rejection of claim 43, Applicant asserts that the additional reference Shum does not teach detecting target analytes in the sample based on the corrected target oligonucleotide sequences (pg. 15, para. 4).
Shum is applied in combination with Press, Schober and Chen. The pending rejection relies on the combined teachings of Press, Schober and Chen for making obvious this feature, as detailed in the rejection.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 USC §§ 102 and 103 is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
Claims 1, 3-8, 11, 13, 15-16, 18, 20-21, 23, 25, 27-32, 37, 41-42 and 44-45 are rejected under 35 USC § 103 as being unpatentable over WIPO Patent Pub. 2019/204702 (effectively filed 4/20/2018; hereafter “Press”; previously cited), as evidenced by MiSeq System User Guide (Part #15027617 H, Illumina, Inc.; published March 2013; hereafter “MiSeq User Guide”; previously cited), in view of Schober et al (Proc 2012 IEEE Int’l Workshop GenSiPS, pp. 31-34, IEEE Xplore; published 4/25/2013; previously cited) and Chen et al (Science 348(6233): aaa6090, pp. 1-14; published 4/9/2015; on IDS filed 11/24/2021; previously cited). The new grounds of rejection presented herein were necessitated by Applicant’s amendment of the claims (filed 10/17/2025).
Claim 1 recites a computer-implemented method for error correction of decoded target barcode sequences, comprising steps of: obtaining an image for each of a plurality of decoding cycles; detecting, in each image, location(s) of barcode probe sequence(s) that are hybridized or bound to target oligonucleotide sequence(s) or segments thereof; decoding target oligonucleotide sequence(s) based on decoding cycles and detected locations; and replacing decoded target oligonucleotide sequence(s) with a known target oligonucleotide sequence or proxy thereof.
The claim further requires that the known target oligonucleotide sequence has a maximum likelihood as computed from a probability distribution that provides probabilities for detecting a given barcode probe sequence at a given location in a given decoding cycle.
With respect to claim 1, Press discloses a computerized method of generating a set of genetic barcodes, for attaching to samples, that provides for decoding erroneous barcodes (Abstract) and includes steps of: generating lists of barcodes (pg. 3, para. 2), wherein an oligonucleotide comprising a barcode sequence can be a probe that specifically hybridizes with a target oligonucleotide (pg. 10, paras. 2 and 4), and sequencing an oligonucleotide pool using a MiSeq machine (pg. 28, para. 4); decoding barcode sequences and identifying corresponding oligonucleotide sequences (pg. 28, paras. 5-6); and error-correcting an observed barcode sequence to a known (‘center’) barcode sequence (pg. 4, para. 2).
Press further discloses application to identification of individual members in heterogenous ensembles of biomolecules based on error-correcting barcodes (pg. 1, para. 4 - pg. 2, para. 1), i.e., detecting presence of analytes based on corrected target oligonucleotide sequences.
MiSeq User Guide discusses features of the MiSeq platform, and states that the MiSeq performs functions of: imaging flow cells during each of a plurality of cycles in a sequencing run (pg. 7, Flow Cell; pg. 20, Real Time Analysis; pg. 52, Number of Cycles), i.e., obtaining an image for each of a plurality of decoding cycles; and defining sequenced cluster positions in each image according to X and Y coordinates (pp. 46-47, Template Generation), i.e., detecting, in each image, location(s) of sequences.
MiSeq User Guide provides evidence that normal operation of a MiSeq machine, as disclosed by Press, involves performance of these claimed functions. Therefore, Press is considered to disclose performance of these functions.
Press further discloses inferring maximum likelihood sequences using paired reads (pg. 28, para. 4). However, the referenced inferring is described as part of the initial sequencing process rather than the decoding (i.e., error-correction) process. Press does not disclose determination of ‘center’ barcodes having a maximum likelihood as computed from a probability distribution. Neither does Press disclose embodiments wherein barcode probe sequences are hybridized or bound to target oligonucleotide sequence(s) or segments thereof in situ.
Schober discusses design of barcodes with error-correction capabilities (pg. 31, Abstract), and teaches decoding an observed sequence (‘received word’) to a known sequence (‘codeword’) having minimal Hamming distance from the observed sequence.
Schober further teaches that decoding according to minimal Hamming distance achieves correction to the sequence with maximal posterior probability (i.e., the known sequence that has the maximum likelihood based on a probability distribution), and is furthermore capable of computational implementation via lookup tables including possible observed sequences and closest known sequences (pg. 32, l. column).
Schober does not teach embodiments wherein barcode probe sequences are hybridized or bound to target oligonucleotide sequence(s) or segments thereof in situ.
Chen discusses multiplexed error-robust fluorescence in situ hybridization, abbreviated as MERFISH (pg. 1, Abstract), and teaches performance using the MiSeq platform (pg. 11, r. column).
With respect to claim 3, Press discloses application to identification of nucleic acid strands, i.e., analyte sequences, in pooled populations (pg. 2, para. 3).
With respect to claim 4, Press discloses application to identification of RNA strands in pooled populations (pg. 2, para. 3) and explicitly states that, as used therein, the term ‘oligonucleotide’ can refer to a linear polymer of RNA monomers (pg. 10, para. 4).
Press does not explicitly reference messenger RNA (mRNA). However, mRNA is a biomolecular species that one of ordinary skill in the art would be able to “at once envisage” from the disclosure of RNA. Therefore, the disclosure of Press is considered to read on the limitations of the instant claim. See MPEP 2131.02 § III.
With respect to claim 5, Press discloses direct and indirect linkage between a polynucleotide comprising a barcode and a small molecule, macromolecule or antibody (pg. 13, para. 3 – pg. 14, para. 1), i.e.,, association of barcode sequences with target analytes.
With respect to claim 6, Press states that, as used therein, the term ‘oligonucleotide’ generally refers to a linear polymer of nucleotide monomers (pg. 10, para. 4).
With respect to claim 7, Press discloses embodiments wherein oligonucleotides comprise smaller polynucleotides of, for example, 2-100 monomeric units (pg. 10, para. 4 – pg. 11, para. 1), i.e., a plurality of segments, each comprising a plurality of nucleotides.
With respect to claim 8, Press discloses application to identification of individual genetic specimens (e.g., RNA strands) in pooled populations, wherein unique barcode sequences couple to each specimen (pg. 1, para. 4) and thereby function as proxies for target analyte sequences.
With respect to claim 11, Press discloses generating non-overlapping ‘decode spheres’, each including one distinct (‘center’) barcode and erroneous (‘corrupt’) barcode sequences within a specified maximum number of edits of the center barcode (pg. 5, para. 6; pg. 16, paras. 2-3; pg. 19, para. 3 – pg. 20, para. 1; Fig 2A); identifying the unique decode sphere in which an observed corrupt barcode exists, and error-correcting the observed barcode to the center barcode of the decode sphere (pg. 4, para. 2). In other words, replacement of a decoded oligonucleotide sequence with a known oligonucleotide sequence from a subset of known sequences that are within a specified pairwise edit distance of the decoded sequence.
Schober discusses design of barcodes with error-correction capabilities (pg. 31, Abstract), and teaches decoding an observed sequence (‘received word’) to a known sequence (‘codeword’) having minimal Hamming distance from the observed sequence.
Schober further teaches that decoding according to minimal Hamming distance achieves correction to the sequence with maximal posterior probability (i.e., the known sequence that has the maximum likelihood based on a probability distribution), and is furthermore capable of computational implementation via lookup tables including possible observed sequences and closest known sequences (pg. 32, l. column).
With respect to claim 13, Press exemplifies user specification of the maximum allowable number of errors (i.e., edit distance) of 2 errors for each of two primers (pg. 32, para. 1), i.e., 4 errors. Press further exemplifies barcodes with an error correction capability comprising 2 errors (pg. 21, Table 1), and also exemplifies error-correction analysis considering only substitution errors (pg. 6, para. 3; Fig. 3C). In this way, Press discloses embodiments utilizing a specified pairwise edit distance of two times a specified error correction capability comprising correction of 2 substitution errors.
Press discusses Hamming distance as a widely-used error-correcting code, often employed in DNA barcoding error-correction strategies (pg. 18, para. 3). Press presents a number of functional advantages that their barcode design scheme (‘FREE’) has over employment of Hamming distance, but nonetheless discloses that Hamming distance can be employed for correction of substitution errors (pg. 5, para. 3; pg. 21, para. 1).
With respect to claims 15-16, Schober teaches that different barcodes can have different distance distributions, resulting in different error correction capabilities (pg. 33, l. column and illustrated in Fig. 2), and exemplifies calculation of the distribution for each barcode (pg. 33, r. column; pg. 34, Table I, column B0 – B8). Calculation for a predetermined number of iterations amount to mere repetition of a disclosed process, and does not patentably distinguish from the teachings of Schober.
With respect to claim 18, Press discloses provision of an error probability distribution by a binomial model (pg. 28, para. 1), and further discloses employment of machine learning techniques with their methods (pg. 41, para. 3). Although Press does not explicitly disclose employment of a machine learning model to provide the error probability distribution, this amounts to mere substitution of one disclosed modeling technique for another disclosed modeling technique and is considered an obvious variant.
With respect to claim 20, Press discloses provision of an error probability distribution by a binomial model (pg. 28, para. 1), and further discloses employment of neural networks with their methods (pg. 41, para. 3). Although Press does not explicitly disclose employment of a neural network to provide the error probability distribution, this amounts to mere substitution of one disclosed modeling technique for another disclosed modeling technique and is considered an obvious variant.
With respect to claim 21, Press discloses embodiments wherein oligonucleotides comprise smaller polynucleotides of 2-100 monomeric units (pg. 10, para. 4 – pg. 11, para. 1), i.e., segments. Press further discloses sequencing an oligonucleotide pool using a MiSeq machine (pg. 28, para. 4).
MiSeq User Guide discusses features of the MiSeq platform, and states that the MiSeq performs functions of: imaging flow cells during each of a plurality of cycles in a sequencing run (pg. 52, Number of Cycles), i.e., obtaining an image for each of a plurality of decoding cycles. MiSeq User Guide indicates that the number of cycles is user-determined (pg. 52, Run Duration). In this way, utilizing a number of imaging cycles equal to a number of oligonucleotide segments is an obvious embodiment of the teachings of Press, as evidenced by MiSeq User Guide.
MiSeq User Guide provides evidence that normal operation of a MiSeq machine, as disclosed by Press, involves performance of these claimed functions. Therefore, Press is considered to disclose performance of these functions.
With respect to claim 23, Schober teaches construction of barcode sequences with prescribed length, a specified minimum pairwise Hamming distance, a maximum homopolymer length, and an upper bound on GC content (pg. 33, l. column). Schober further teaches functional advantages to sequence selection with these constraints, e.g., high GC content and homopolymers cause enzymatic issues (pg. 33, l. column).
With respect to claim 25, Press exemplifies user specification of the maximum allowable number of errors (i.e., edit distance) of 2 errors for each of two primers (pg. 32, para. 1), i.e., 4 errors. Press further exemplifies barcodes with an error correction capability comprising 2 errors (pg. 21, Table 1), and also exemplifies error-correction analysis considering only substitution errors (pg. 6, para. 3; Fig. 3C). In this way, Press discloses embodiments utilizing a specified pairwise edit distance of two times a specified error correction capability comprising correction of 2 substitution errors.
Press discusses Hamming distance as a widely-used error-correcting code, often employed in DNA barcoding error-correction strategies (pg. 18, para. 3). Press presents a number of functional advantages that their barcode design scheme (‘FREE’) has over employment of Hamming distance, but nonetheless discloses that Hamming distance can be employed for correction of substitution errors (pg. 5, para. 3; pg. 21, para. 1).
With respect to claims 27-28, Press discloses embodiments wherein oligonucleotides comprise smaller polynucleotides of 2-100 monomeric units (pg. 10, para. 4 – pg. 11, para. 1), i.e., at least two segments, with lengths of at least two nucleotides.
With respect to claim 29, Press discloses selection of barcode sequences according to sequence constraints including GC content of 40-60% (pg. 20, para. 2).
The disclosed range, 40-60%, overlaps the claimed range of ≤ ~50% GC content. Where prior art discloses a range which overlaps or approaches a claimed range, the prior art disclosure renders the claimed range as obvious (MPEP 2144.05 § I).
With respect to claim 30, Press discloses selection of barcode sequences according to sequence constraints including disallowance of homopolymer triplets (pg. 20, para. 2; pg. 26, para. 5), i.e., a specified maximum length for homopolymer subsequences of 2 nucleotides.
The disclosed range, ≤ 2, falls within the claimed range of ≤ 7 nucleotides. Where prior art discloses a range which overlaps or approaches a claimed range, the prior art disclosure renders the claimed range as obvious (MPEP 2144.05 § I).
With respect to claim 31, Chen discusses multiplexed error-robust fluorescence in situ hybridization, abbreviated as MERFISH (pg. 1, Abstract), and teaches utilization of a modified Hamming distance-based image decoding scheme wherein fluorescent spots detected in multiple cycles were used to construct a binary word indicating the on-off (1-0) status of each spot in each cycle, and only four matching 1-bits per word were considered in decoding words to RNA species (pg. 1, r. column; pg. 11, m. column).
Chen discloses that constructed binary words with zero differences from a code word (i.e., known barcode sequence) were interpreted as exact matches, while binary words differing by one bit (i.e., having a 0-bit among the considered four bits per word) were interpreted as error-correctable matches and decoded accordingly (pg. 2, r. column). Chen therein discloses embodiments of their technique wherein at least one segment of each sequence encodes for an ‘OFF’ state that is not visualized in at least one cycle.
Chen teaches that MERFISH allows for effective multiplexed image processing and error correction for sets of over 1,000 genes, and has potential for computationally-feasible scaling to address the entire human transcriptome (pg. 7, r. column).
With respect to claim 32, Chen exemplifies utilizing 32-bit binary code words (pg. 6, l. column). Consideration of only four bits per each 32-bit word, representing fluorescent spot visualizations, is consideration of only 12.5% of total visualized information. This is considered equivalent to a ‘dilution factor’ of 87.5%.
With respect to claim 37, Press discloses a barcode list including >106 unique barcodes (pg. 3, para. 1), i.e., a total number of unique barcode sequences of at least 1000.
With respect to claim 41, Press discloses generating lists of barcodes (pg. 3, para. 2), and further discloses embodiments wherein an oligonucleotide comprising a barcode sequence can be a probe that specifically hybridizes with a target oligonucleotide (pg. 10, paras. 2 and 4) and can be immobilized on a solid support (pg. 13, para. 4 – pg. 14, para. 1; pg. 14, para. 4 – pg. 15, para. 1). In this way, Press discloses embodiments wherein barcode sequences are incorporated into a set of target-specific probe molecules.
With respect to claim 42, Press discloses embodiments wherein an oligonucleotide comprising a barcode sequence is immobilized on a solid support (pg. 13, para. 4 – pg. 14, paras. 1 and 4), and further discloses sequencing an oligonucleotide pool using a MiSeq machine (pg. 28, para. 4).
MiSeq User Guide states that the MiSeq performs sequencing of samples loaded onto flow cells comprising a glass-based substrate, that are divided into small imaging areas called tiles; provides a graphic representation of sequenced cluster density per tile; and defines sequenced cluster positions in each image according to X and Y coordinates (pg. 7, Flow Cell; pp. 45-47, Sequencing Screen and Template Generation).
Thus, Press discloses that each barcode sequence can be attached to a substrate and MiSeq User Guide provides evidence that normal operation of a MiSeq machine, as disclosed by Press, involves sequencing of nucleic acids loaded onto different features (e.g., tiles) of a spatial array substrate. Therefore, Press is considered to disclose embodiments wherein each unique nucleic acid barcode sequence is attached to a different feature of a spatial array.
Claim 44 is directed to a system comprising one or more processors, memory operably coupled to the processor(s), and stored programs that, when executed by the processor(s), cause the system to execute functions corresponding to steps of the method of claim 1.
With respect to claim 44, the teachings of Press, Schober and Chen are considered to read on the recited functional limitations in the same way as indexed above with respect to the substantively similar process limitations of claim 1.
Press additionally discloses system embodiments comprising computer hardware and software including: a processing unit that communicates with other elements, memory and a memory controller, and stored computer program instructions that implement functions of the disclosed methods (pg. 38, paras. 2-4; pg. 39, paras. 2 and 4).
Claim 45 is directed to a non-transitory computer-readable storage medium storing one or more programs comprising instructions which, when executed by one or more processors of a computing platform, cause the computing platform to perform functions corresponding to steps of the method of claim 1.
With respect to claim 45, the teachings of Press, Schober and Chen are considered to read on the recited functional limitations in the same way as indexed above with respect to the substantively similar process limitations of claim 1.
Press additionally discloses program product embodiments comprising computer-readable media, such as a CD-ROM, having instructions stored thereon that cause a general purpose computer to perform functions that accomplish steps of the disclosed methods (pg. 36, para. 5 – pg. 37, para. 1).
An invention would have been obvious to one of ordinary skill in the art if some teaching in the prior art would have led that person to combine prior art reference teachings to arrive at the claimed invention. Before the effective filing date of the claimed invention, said practitioner would have implemented determination of barcode sequences having a maximum likelihood as computed from a probability distribution, as taught by Schober, in combination with the error-correction methodology of Press, because Schober teaches that their technique achieves effective correction of observed sequences and can be computationally implemented via lookup tables (pg. 32, l. column). Said practitioner would have had a reasonable expectation of success because Press and Schober both discuss error-correction and barcoding methods.
An invention would have been obvious to one of ordinary skill in the art if some teaching in the prior art would have led that person to combine prior art reference teachings to arrive at the claimed invention. Before the effective filing date of the claimed invention, said practitioner would have implemented a visualization and decoding scheme including consideration of a non-visualized ‘off’ state, as taught by Chen, in combination with the error-correction methodology of Press, because Chen teaches that their imaging-based, sparse decoding strategy effectively achieves simultaneous image processing and error correction for vast sets of genes (pg. 7, r. column). Said practitioner would have had a reasonable expectation of success because Press and Chen both discuss image-based barcoding and error-correction methods.
In this way the disclosure of Press, as evidenced by MiSeq User Guide, in view of Schober and Chen, makes obvious the limitations of claims 1-8, 11, 13, 15-16, 18, 20-21, 23, 25, 27-32, 37, 41-42 and 44-45. Thus, the invention is prima facie obvious.
Claim 43 is rejected under 35 USC § 103 as being unpatentable over Press, as evidenced by MiSeq User Guide, in view of Schober and Chen, as applied to claim 23 above, and further in view of Shum et al (US 2019/0095578; effectively filed 9/5/2017; previously cited). The new grounds of rejection presented herein were necessitated by Applicant’s amendment of the claims (filed 10/17/2025).
With respect to claim 43, Press discloses embodiments wherein an oligonucleotide comprising a barcode sequence is immobilized on a bead (pg. 13, para. 4 – pg. 14, paras. 1 and 4). However, Press does not disclose embodiments wherein each unique nucleic acid barcode sequence is attached to a different bead of a bead array.
Schober exemplifies application to data from Illumina sequencing platforms (pg. 31, r. column). Schober does not teach embodiments wherein each unique nucleic acid barcode sequence is attached to a different bead of a bead array.
Chen discusses the inclusion of beads for use as fiducial markers (pg. 10, m. column). Chen does not describe embodiments wherein each unique nucleic acid barcode sequence is attached to a different bead of a bead array.
Shum discusses methods and systems for determining occurrences of molecular target sequences (Abstract), and teaches barcode sequences comprising nucleic acid sequences called ‘spatial labels’ that provide information about target molecule coordinate location within a sample (para. 0105). Shum further teaches embodiments wherein a spatial label is different for barcodes attached to different beads (para. 0106). In other words, each unique nucleic acid barcode sequence is attached to a different bead of a bead array.
An invention would have been obvious to one of ordinary skill in the art if some teaching in the prior art would have led that person to combine prior art reference teachings to arrive at the claimed invention. Before the effective filing date of the claimed invention, said practitioner would have implemented attachment of barcodes to different beads of a bead array, as taught by Shum, in combination with the error-correction methodology of Press, in view of Schober and Chen, because Press exemplifies use of the MiSeq platform, and immobilization of probes on a bead, while Shum teaches that attachment to different beads allows for provision of spatial location information (as required by the imaging processing operation of the MiSeq platform disclosed by Press). Said practitioner would have had a reasonable expectation of success because Press and Shum both discuss nucleic acid sequencing methods.
In this way the disclosure of Press, as evidenced by MiSeq User Guide, in view of Schober, Chen and Shum, makes obvious the limitations of claim 43. Thus, the invention is prima facie obvious.
Conclusion
At this point in prosecution, no claim is allowed.
The following prior art, made of record and not relied upon, is considered pertinent to applicant’s disclosure:
Shah et al (ACS Synth. Biol. 8: 1100-1111; published 4/5/2019) discusses optical multiplexing using fluorescent, error-correcting barcodes and machine learning (pg. 1101, Abstract; pg. 1109, r. column); and
Zhuang et al (US 2022/0064697; effectively filed 12/13/2018) discloses systems and methods for imaging or determining nucleic acids in cells or other samples utilizing MERFISH error correction (Abstract; para. 0057).
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 nonprovisional extension fee (37 CFR 1.17(a)) 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 mailing date of this final action.
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/T.C.S./Examiner, Art Unit 1685
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686