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 .
Election/Restrictions
Applicant’s election without traverse of Group I, encompassing claims 1-15 and 20-22 in the reply filed on May 12th, 2026 is acknowledged.
Claims 30 and 33 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on April 27th, 2026.
Claim Status
Claims 16-19, 23-29, 31-32, and 34-35 have been canceled. Claims 1-15, 20-22, 30, and 33 are pending. Claims 30 and 33 are withdrawn as being drawn to a non-elected invention/species. Claims 1-15 and 20-22 are under examination and discussed in this Office Action.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on March 12th, 2024, November 19th, 2024, and December 11th, 2024 are acknowledged. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code on page 105. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 6 and 10 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.
Claim 6 recites the limitation “…generating a signal is between 1.25:1 to 5:1, preferably between 1.5:1 to 3:1, more preferably about 2:1.” The use of “preferably” and “more preferably” renders the claim scope indefinite it is unclear whether the narrower ranges between 1.5:1 to 3:1 and about 2:1 respectively, constitute actual claim limitations or merely identify preferred embodiments within the broader recited range of 1.25:1 to 5:1. It is unclear which controls. The instant specification also uses the same language (p. 2, line 33-36).
Claim 10 recites the limitation “…light emissions from the second labeled primers are emitted from the same region or substantially overlapping regions of the substrate.” It is unclear what degree of spatial overlap between light emitting regions of the substrate is required to satisfy this limitation. While the instant specification defines “substantially” as indicating that a result is close to a targeted value, where close can mean within 80%, 90%, 95%, or 99% of the value (p. 103, para 4). This definition is directed to quantitative measurement values and does not map to a spatial relationship between light emission region on a substrate. The instant specification uses the phrase “substantially overlapping regions (p. 3; p. 7; p. 9; and 71) without providing an objective threshold for what degree of spatial overlap qualifies, leaving the scope of this limitation uncertain.
Claim Rejections - 35 USC § 101
35 U.S.C. 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 1-15 and 20-22 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon and an abstract idea without significantly more. While the claims are directed to processes, and therefore meet step 1 of the subject matter eligibility test (see MPEP 2106.03), the claims recite abstract idea of mathematical classification of numerical data including obtaining numerical intensity values, selecting one of a plurality of predetermined classifications based on those values, and using the selected classification to determine an output. This is a mathematical concept because it consists of applying a classification algorithm to numerical inputs to generate an output, which can be performed by a mathematical operation or in the human mind.
Step 2A of the subject matter eligibility test requires a two-pronged analysis. Prong One asks: does the claim recite an abstract idea, law of nature or natural phenomenon? As discussed in MPEP 2106.04(II)(A)(1), the meaning of "recites" is "set forth" or "describes". That is, a claim recites a judicial exception when the judicial exception is "set forth" or "described" in the claim. In the instant case, the claims describe an abstract idea (a mathematical concept of data classifications. Steps (a) and (b) of claim 1 recite obtaining numerical intensity values (data gathering). Step (c) recites selecting one of a plurality of classifications based on those numerical values (mathematical classification). Step (d) recites base calling the respective nucleobases based on the selected classification (drawing a conclusion from the classification output)).
Prong Two of the analysis under step 2A asks: does the claim recite additional elements that integrate the judicial exception into a practical application of the judicial exception? As discussed in MPEP 2106.04(II)(A)(2), "Because a judicial exception is not eligible subject matter, Bilski, 561 U.S. at 601, 95 USPQ2d at 1005-06 (quoting Chakrabarty, 447 U.S. at 309, 206 USPQ at 197 (1980)), if there are no additional claim elements besides the judicial exception, or if the additional claim elements merely recite another judicial exception, that is insufficient to integrate the judicial exception into a practical application. See, e.g., RecogniCorp, LLC V. Nintendo Co., 855 F.3d 1322, 1327, 122 USPQ2d 1377 (Fed. Cir. 2017) ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non- abstract"); Genetic Techs. V. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016) (eligibility "cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself."). For a claim reciting a judicial exception to be eligible, the additional elements (if any) in the claim must "transform the nature of the claim" into a patent-eligible application of the judicial exception, Alice Corp., 573 U.S. at 217, 110 USPQ2d at 1981, either at Prong Two or in Step 2B." The considerations to be used are set forth at MPEP 2106.05(a) through (c) and (e) through (h). Turning to those sections of the MPEP:
MPEP 2106.05(a) has to do with improvements to the functioning of a computer or to any other technology or technical field. The claims at issue do not improve the functioning of a computer or other technology. The instant claims recite obtaining intensity data, selecting a classification, and base calling use existing mathematical and computational techniques without improving any technology. The absence of physical sequencing steps in these claims means there is no improvement to the sequencing technology being claimed.
MPEP 2106.05(b) has to do with whether the claims involve the use of a particular machine. In this case, the claims do not involve the use of a particular machine. No sensor, sequencer, flow cell, optical system, or computing hardware is recited in these claims. Even claim 21 recites a Gaussian mixture model and that does not that tie that mathematical technique to any particular machine.
MPEP 2106.05(c) has to do with whether the claims involve a particular transformation. Here, none of the limitations of the claims involve a particular transformation.
MPEP 2106.05(e) has to do with "other meaningful limitations". The additional limitations imposed upon the abstract idea in the claims consist of obtaining intensity data and determining a nucleobase output from a classification result. These are not meaningful limitations because they amount to applying the mathematical classification to a specific type of numerical data (intensity values from sequencing) and using the output for a specific purpose (base calling).
MPEP 2106.05(f) raises the question as to whether the additional elements recited in the claim represent "mere instructions to apply an exception". The steps of obtaining intensity data in steps (a) and (b) is data-gathering activity that serves as the input to the mathematical classification of step (c). The base calling step (d) is the output of the mathematical classification. These additional elements do amount to mere instructions to apply the mathematical classification to intensity data from sequencing, which is mere instruction to apply the abstract idea in a particular context.
MPEP 2106.05(g) has to do with whether the additional elements of the claim amount to insignificant extra-solution activity. MPEP 2106.05(g) notes that "[d]etermining the level of a biomarker in blood" is an example of "mere data gathering" which the courts have found to be insignificant extra - solution activity. The step of obtaining intensity data in steps (a) and (b) is data-gathering activity that the courts have recognized as insignificant extra-solution activity.
MPEP 2106.05(h) has to do with whether the additional elements amount to more than generally linking the use of a judicial exception to a particular technological environment or field of use. The recitation of the method being applied to polynucleotide sequence portions and intensity data from sequencing represents a “field of use” limitation. The mathematical classification is applied to sequencing data. However, as MPEP 2106.05(h) indications, such limiting to a particular “field of use” does not confer patentability on otherwise ineligible subject matter.
Regarding claim 21, the Gaussian mixture model recited is a mathematical technique. Reciting a specific mathematical algorithm as the means of performing the abstract classification step of claim 1 (c) adds a more specific mathematical concept to the abstract idea and does not integrate the exception into a practical application.
In addition, the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception (as set forth in step 2B of the subject matter eligibility test; see MPEP 2106-III) because it was known in the prior art to obtain combined intensity data from simultaneous primer extensions on co-localized polynucleotide sequence portions, classify those combined intensity values inti a set of predetermined categories, and determine nucleotide identity from the classification results. Shi et al (US8126235B2; issued February 28th, 2012) teaches performing automated base-calling on multiple DNA strands using intensity information from a chemical sequencing process performed simultaneously on a plurality of DNA strands, obtaining a function incorporating intensity information corresponding to each of the plurality if DNA strands, identifying peaks in that function, and assigning membership to each peak by determining whether each peak resulted from none, one, or multiple of the plurality of DNA strands (claim 1; claim 5), which is a classification of combined intensity data into predetermined categories. Boutell (US20170298430A1; published October 19th, 2017) further teaches obtaining combined signal intensity data from simultaneous primer extensions on two or more polynucleotide portions and using histograms to allocate base calls from the combined signal [0119-0121; claims 1, 13, 14].
Having considered the factors discussed in MPEP 2106.05 (a)-(c) and (e)-(h), as well as the prior art of Shi and Boutell, it is clear that the additional elements recited in the claims, whether considered individually or as a combination, do not integrate the judicial exceptions into a practical application of those exceptions in such a way as to provide meaningful limits on the use of the judicial exceptions. Therefore, claims 1-15 and 20-22 are rejected here under 35 U.S.C. 101.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 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.
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 1-15 and 20-22 are rejected under 35 U.S.C. 103 as being unpatentable over Boutell (US20170298430A1; published October 19th, 2017) in view of Shi (US8126235B2; issued February 28th, 2012).
Regarding instant claim 1, Boutell teaches a method of base calling nucleobases of two or more polynucleotide sequence portions comprising:
Obtaining first intensity data comprising a combined intensity of a first signal obtained based upon a respective first nucleobase of at least one first polynucleotide sequence portion and a second signal obtained based upon a respective second nucleobase of at least one second polynucleotide sequence portion, wherein Boutell teaches that intensity histograms show that the combined signals result in different intensity information being obtained which can then be allocated to base information to allow effective base calling [0119-0120].
Obtaining second intensity data comprising a combined intensity of a third signal obtained based upon the respective first nucleobase of the at least one first polynucleotide sequence portion and a fourth signal obtained based upon the respective second nucleobase of the at least one second polynucleotide sequence portion wherein Boutell teaches that T incorporation on SBS3 shows up as strong signal in green and orange channels, very weak in red, and incorporation of A on SBS8′ shows up as strong in orange and red channels [0119], establishing that the combined signal from both primer extensions is detected across multiple non- identical optical channels, providing the second intensity data in a second optical channel as required by step b). Boutell further teaches the signal data is detected as colour signals corresponding to a plurality of nucleotide analogues incorporated the primer extensions and wherein each colour signal corresponds to a different nucleotide analogue or combination of nucleotide analogues [0036; (claim 16)].
Selecting one of a plurality of classifications based on the first and the second intensity data, wherein each classification of the plurality of classifications represents a possible combination of respective first and second nucleobases, wherein Boutell teaches using combined intensity histograms to identify nucleobases from simultaneous primer extensions [0121], where the combined histogram encompasses classification regions that represent multiple possible nucleobase combinations. However, Boutell does not explicitly formalize a predefined classification space with the structural property that at least one class covers multiple combinations.
Shi, in the same field of endeavor, teaches a predefined classification framework for base calling from combined intensity data from multiple simultaneously sequenced DNA strands. Shi teaches assigning membership to each of the plurality of peaks by determining whether each of the plurality of peaks is believed to have resulted from none, one or multiple of the plurality of DNA strands (claim 1). Shi further teaches that the membership assignment determining whether each of the plurality of peaks belongs to none, the first DNA strand, the second DNA strand or both the first DNA strand and the second DNA strand (claim 4). This is a formal predefined classification space of exactly four possible membership classes, where the category where a peak belongs to both the first and second DNA strand explicitly represents a classification covering more than one possible nucleobase combination, directly teaching that at least one classification represents more than one possible combination of respective first and second nucleobases. Shi further teaches that the controller is configured to determine the probability by factoring the function into a factor graph and traversing the factor graph to determine the probability that each of the plurality of peaks resulted from none, one or multiple DNA strands based, at least in part, on the peak amplitudes and peak locations (claim 19), establishing the probabilistic nature of the classification framework.
Based on the selected classification, base calling the respective first and second nucleobases, wherein said polynucleotide sequence portions have been selectively processed such that an intensity of the signals obtained based upon the respective first nucleobase is greater than an intensity of the signals obtained based upon the respective second nucleobase, wherein Boutell teaches allocating base calls to extension reads based on the combined intensity classification [0122; claim 1]. Boutell discloses that “each call at each position will then need to be allocated to the correct extension read” [0122] and “determining from said signal data the identity of the nucleotide bases and allocating said bases to an extension read” (claim 1).
Boutell further teaches that one method of allocating base calls to the correct extension read is making one of the reads brighter than the other by using a mixture of blocked and unblocked primer [0122], and provides a specific embodiment wherein primer 1 is 100% unblocked yielding 100% signal intensity while primer 2 is 25% unblocked and 75% blocked yielding 25% signal intensity, resulting in two reads generating data at two different intensity levels [0124]. Boutell further teaches the use of blocked and unblocked primers to chemically differentiate between extension reads (claim 11; [0067-0068]).
Shi further teaches computing a sequence for the at least one base for each of the plurality of DNA strands based, at least in part, on the membership assignment (claim 1).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have combined the simultaneous dual-primer sequencing with controlled differential intensity of Boutell with the probabilistic peak classification framework of Shi. Both references address the same technical problem of base calling from combined optical signals generated by simultaneously sequencing multiple polynucleotide portions. One of ordinary skill in the art would have been motivated to combine these teachings because applying the classification framework of Shi to the combined intensity data of Boutell provides a systematic method for assigning base calls from mixed signals, yielding predictable improvements in accuracy and reliability. The combination represents the application of a known technique to a known problem with a reasonable expectation of success.
Regarding instant claim 2, Boutell, in view of Shi, teaches the method of claim 1 wherein the first and second signals and/or the third and fourth signals are obtained substantially simultaneously. Boutell teaches the plurality of extension reads comprise substantially simultaneous extension reads (claim 4). Boutell further teaches that the signal data corresponding to each of the at least two primer extensions is obtained substantially simultaneously (claim 13).
Shi further teaches a chemical sequencing process performed simultaneously on a plurality of DNA strands (claim 1).
Regarding instant claim 3, Boutell, in view of Shi, teaches the method of claim 1 wherein selecting the classification is based on the combined intensity of the first and second signals and the combined intensity of the third and fourth signals. Boutell teaches that the signal intensity profile is analyzed across multiple optical channels simultaneously, wherein the combined intensity across both detection channels at each cycle forms the basis for base calling (claim 14; [0072-0073]).
Shi further teaches that the classification function is based on combined intensities from both strands across all detection channels (claim 4). Shi stated, “the function includes the superposition of information from the first DNA strand and the second DNA strand,” establishing that the combined intensity from both channels is incorporated into a single classification function.
Regarding instant claim 4, Boutell, in view of Shi, teaches the method of claim 1 wherein the plurality of classification comprises sixteen classifications, each classification representing one of sixteen unique combinations of first and second nucleobases. The four canonical nucleobases applicable to each of the two simultaneously sequenced portions yield 4 X 4 = 16 possible pairwise combinations. Applying the classification framework of Shi to the two-strand simultaneous sequencing system of Boutell, a person of ordinary skill in the art would recognize that a complete classification space covering all possible nucleobase combinations across the two sequence portions contains exactly sixteen classes. This is a direct mathematical consequence of the state space defined by the combined teachings.
Regarding instant claim 5, Boutell, in view of Shi, teaches the method of claim 1 wherein the polynucleotide sequence portions have been selectively processed such that, during sequencing, a greater number of the first polynucleotide sequence portions are capable of generating a signal than the second. Boutell teaches differential processing via a blocked/unblocked primer mixture such that a greater number of first polynucleotide sequence portions are capable of generating signal than second polynucleotide sequence portions. The 100%/25% blocked primer embodiment [0124], directly establishes this differential in signal-capable portions between the two simultaneously sequenced populations.
Regarding instant claim 6, Boutell, in view of Shi, teaches the method of claim 5 wherein a ratio between the number of the first polynucleotide sequence portions capable of generating a signal and the number of the second polynucleotide sequence portions capable of generating a signal is between 1.25:1 to 5:1, preferably between 1.5:1 to 3:1, more preferably about 2:1. Boutell teaches controlling the ratio of blocked to unblocked primers to achieve a target differential between signal-capable population [0124]. The specific 100%/25% embodiment corresponds to a 4:1 ratio, which falls within the 1.25:1 to 5:1 range [0124].
Shi further teaches that an exemplar amplitude ratio of approximately 2:1 between the major and minor traces is used (column 5, para 5 – column 6, para 1), directly teaching the preferred 2:1 ratio. Selection of a specific ratio within the claimed range represents routine optimization and would have been within the skill of a person of ordinary skill in the art.
Regarding instant claim 7, Boutell, in view of Shi, teaches the method of claim 1 wherein the first signal, second signal, third signal and fourth signal are generated based on light emissions associated with the respective nucleobase. Boutell teaches sequencing by synthesis using fluorescently labeled nucleotide analogues wherein the signals are optical emissions from labels incorporated at each sequencing cycle [0051; 0061; claim 2]).
Regarding instant claim 8, Boutell, in view of Shi, teaches the method of claim 7 wherein the signals are generated by contacting polynucleotide molecules with first and second primers, extending the primers with labeled nucleobases, stimulating the light emissions, and detecting them at a sensor. Boutell teaches contacting the nucleic acid with an enzyme in the presence of at least two primers able to hybridise to the same strand at different positions and four labeled nucleotide analogues under conditions permitting hybridization to give a plurality of extension reads, removing unbound labelled moieties, determining the identity of the incorporated nucleotide analogues via their unique labels, and allocating the bases to an extension read (claim 2; claim 1; [0029-0030]). Stimulation of fluorescent labels and detection at a sensor is inherent to the fluorescent-based SBS method disclosed by Boutell [0061; 0051]
Regarding instant claim 9, Boutell, in view of Shi, teaches the method of claim 8 wherein the firs tand second signals are based on light emissions detected in a first range of optical frequencies, the third and fourth signals in a second range of optical frequencies, and the ranges are not identical. Boutell teaches detection via colour signals corresponding to different nucleotide analogues across distinct optical channels, wherein each colour signal corresponds to a different nucleotide analogue or combination of nucleotide analogues (claim 16; [0075]). Boutell further teaches the three channel detection scheme (green, orange, and red channels) which demonstrates detection across distinct, non-identical optical frequency ranges [0119-0120].
Regarding instant claim 10, Boutell, in view of Shi, teaches the method of claim 8 wherein the polynucleotide molecules are attached to a substrate and the light emissions from the first and second labeled primers are emitted from the same region or substantially overlapping regions of the substrate. Boutell teaches polynucleotide nucleic acids bound to a solid support such as a chip or bead (claim 7; [0055-0058]). Boutell further teaches that the two simultaneously sequenced extension reads originate from the same nucleic acid strand bound to the same location on the support (claim 1; [0052]). Light emissions from both labeled primers therefore originate from the same region of the substrate.
Regarding instant claim 11, Boutell, in view of Shi, teaches the method of claim 8 wherein the light emissions detected at the sensor are spatially unresolved. Boutell teaches that the signals from both extension reads appear as combined intensity in the same histogram, with no spatial separation between the two contributions [0120-0121]. The two simultaneous extension reads originate from the same nucleic acid strand bound to the same location on the support, and the fluorescent signals from both primers are emitter from the same cluster and are spatially unresolved at the detector.
Shi further teaches that the function includes the superposition of information from both DNA strands (claim 4), which is inherently a spatially unresolved composite signal.
Regarding instant claim 12, Boutell, in view of Shi, teaches the method of claim 11 wherein the sensor is configured to provide a single output based upon the first and second signals. Boutell teaches combined intensity histograms which represent a single sensor output from a single cluster location encompassing contributions from both extension reads [0120-0121].
Shi similarly describes the composite trace as a single function incorporating the superposed intensity from both DNA strands (claim 1; claim 4).
Regarding instant claim 13, Boutell, in view of Shi, teaches the method of claim 8 wherein the sensor comprises a single sensing element. Boutell teaches cluster-based detection on a solid support wherein each cluster is imaged by the detection system as a single location, producing a combined output from all sequence portions in that cluster (claim 15; [0052]).
Regarding instant claim 14, Boutell, in view of Shi, teaches the method of claim 8 wherein each polynucleotide molecule comprises one or more copies of the first polynucleotide sequence portion and one or more copies of the second polynucleotide sequence portion. Boutell teaches hybridising at least two primers to the same strand of nucleic acid (claim 1), meaning the same nucleic acid molecule carries both the first and second polynucleotide sequence portions. Boutell further teaches that the nucleic acid is amplified on a solid support into a cluster, each molecule in the cluster carries copies of both portion [0062-0063].
Regarding instant claim 15, Boutell, in view of Shi, teaches the method of claim 1 wherein the first and second polynucleotide sequence portions are respective portions of different polynucleotide molecules. Boutell teaches that at least two primers hybridize to the same strand at different positions (claim 1), giving extension reads that represent distinct portions of the nucleic acid. These distinct portions can be considered portions of different polynucleotide molecules where the strand is treated as a template for independent extension reads.
Regarding instant claim 20, Boutell, in view of Shi, teaches the method of claim 1 wherein the at least one first polynucleotide sequence portion and the at least one second polynucleotide sequence portion are present in a cluster. Boutell teaches performing simultaneous multi primer sequencing on polynucleotide sequence portions immobilized on a solid support, amplified into clusters by bridge amplification, and imaged as cluster-level intensity signals [0062-0063; 0052]
Regarding instant claim 21, Boutell, in view of Shi, teaches the method of claim 1 wherein the classifications is selected using a Gaussian mixture model. Shi teaches that the membership assignment is performed by estimating peak amplitudes and locations, determining the probability that each peak resulted from none, one, or multiple strands using a factor graph, and applying a Sum-Product algorithm to determine those probabilities (claims 8-9). It would have been obvious to implement this probabilistic classification step using a Gaussian mixture model as the specific framework, as Gaussian mixture model were a standard tool for probabilistic intensity-based classification.
Claim 22 are rejected under 35 U.S.C. 103 as being unpatentable over Boutell (US20170298430A1; published October 19th, 2017) in view of Shi (US8126235B2; issued February 28th, 2012), as applied to claim 1 above, and further in view of Smith WO2007010252A1; published January 25th, 2007).
Regarding instant claim 22, Boutell, in view of Shi, teaches the method of claim 1.
Boutell and Shi do not teach determining that the second polynucleotide sequence portion is modified relative to the first based on the selected classification. Neither Boutell nor Shi discloses using a mismatch classification to identify a sequence modification such as cytosine methylation.
Smith, in the same field of endeavor, teaches pairwise sequencing of a first and second region of target double-stranded polynucleotide derived from the same original molecule, wherein differences between the sequence reads from the two regions constitute meaningful sequence information about the target molecule (claim 1).
It would have been obvious to one of ordinary skill in the art to apply the combined intensity classification framework of Boutell and Shi to the paired strand sequencing approach of Smith and to recognize that a mismatch classification between the forward and reverse complement strands of the same target molecule is indicative of a sequence modification at that position. All three references are directed to the same technical field of sequencing multiple polynucleotide portions simultaneously from the same molecule or cluster, and apply the mismatch classification output to detect sequence differences between paired strands is a predictable and logical extension of the combined teachings.
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 filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual 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/apply/applying-online/eterminal-disclaimer.
Claims 1-15 and 20-22 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-8, 11, 13, 15, 17-18, 20-24, 29, and 32 of copending Application No. 18/573,965 (US20250263790A1), in view of Shi (US8126235B2; issued February 28th, 2012).
Although the claims at issue are not identical, they are not patentably distinct from each other because both the ‘965 and the instant application are directed to the same core inventive concept of simultaneously sequencing two polynucleotide sequence portions co-localized within the same cluster on a substrate on a substrate, detecting the combined light emissions from both sets of labeled primers across two non-identical optical frequency ranges, and determining nucleobase identity based on the combined intensity of the signals from both primer sets.
Claim 1 of the ‘965 application teaches: (a) obtaining first intensity data comprising a combined intensity of a first signal obtained based upon a respective first nucleobase of at least one first polynucleotide sequence portion and a second signal obtained based upon a respective second nucleobase of at least one second polynucleotide sequence portion; (b) obtaining second intensity data comprising a combined intensity of a third signal and a fourth signal based upon the respective first and second nucleobases; (c) selecting one of a plurality of classifications based on the first and the second intensity data, wherein each classification of the plurality of classifications represents one or more possible combinations of respective first and second nucleobases, and wherein at least one classification of the plurality of classifications represents more than one possible combination of respective first and second nucleobases; (d) based on the selected classification, determining sequence information from the at least one first polynucleotide sequence portion and the at least one second polynucleotide sequence portion. These steps directly correspond to steps a) through d) of instant claim 1.
The instant claim 1 requires that the polynucleotide sequence portions have been selectively processed such that an intensity of the signals obtained based upon the respective first nucleobase is greater than an intensity of the signals obtained based upon the respective second nucleobase, whereas claim 1 of the ‘965 application does not recite this differential intensity limitation.
However, Shi teaches this limitation. Shi teaches that the chemical sequencing process applies a different concentration of reagent to each of the plurality of strands so that the average peak intensity for peaks arising from each of the plurality of DNA strands are different, wherein the function comprises a superposition of the intensity information from the plurality of DNA strands (claim 7). This teaching of Shi renders it obvious to modify the classification framework of ‘965 application to include selective processing producing differential signal intensity between the two sequence portions as required by the instant claim 1 d). One of ordinary skill in the art would have been motivated to make this modification because differential intensity between the two simultaneously sequenced portions facilitates reliable allocation of combined base calls to the correct extension read, as taught by Shi. Any additional limitations of the claims of the instant application claims are encompassed by the open claim language “comprising” and are further rendered obvious by Shi as discussed in the 35 USC § 103 rejections above.
Regarding instant claim 2, claim 2 of the ‘965 application teaches obtaining the first and second signals substantially simultaneously, directly corresponding to instant claim 2.
Regarding instant claim 3, claim 3 of the ‘965 application teaches selecting the classification based on the combined intensity of the first and second signals and the combined intensity of the third and fourth signals, directly corresponding to instant claim 3
Regarding instant claim 4, claim 4 of the ‘965 application teaches that when based on a nucleobase of the same identity, an intensity of the first signal is substantially the same as an intensity of the second signal and an intensity of the third signal is substantially the same as an intensity of the fourth signal. This corresponds to the sixteen-classification framework of instant claim 4.
Regarding instant claim 5, claim 5 of the ‘965 application teaches that the plurality of classifications consists of a predetermined number of classifications, directly corresponding to instant claim 5.
Regarding instant claims 6, no claim of the ‘965 application directly recites the ratio limitation of 1.25:1 to 5:1 between single capable first and second polynucleotide sequence portions. However, Shi teaches that an amplitude ration of approximately 2:1 between the major and minor traces is used in simultaneous multi-strand sequencing (column 5, para 5 – column 6, para 1), which falls within the claimed range. The selection of a specific ratio within the 1.25:1 to 5:1 range is rendered obvious by Shi as discussed in the 35 USC § 103 rejections above.
Regarding instant claim 7, claim 15 of the ‘965 application teaches the first signal, second signal, third signal and fourth signal are generated based on light emissions associated with the respective nucleobase and detected at a sensor, directly corresponding to instant claim 7.
Regarding instant claim 8, claim 15 of the ‘965 application teaches contacting a plurality of polynucleotide molecules with first and second primers, extending the first and second primers stimulating the light emissions, and detecting the light emissions at a sensor, directly corresponding to the physical sequencing steps of instant claim 8.
Regarding instant claims 9, claim 17 of the ‘965 application teaches that the first and second signals are based on light emissions detected in a first range of optical frequencies and the third and fourth signals are based on light emissions detected in a second range of optical frequencies, wherein the ranges are not identical, directly corresponding to instant claim 9.
Regarding instant claim 10, claim 18 of the ‘965 application teaches that the polynucleotide molecules are attached to a substrate and the light emissions from the first and second labeled primers are emitted from the same region or substantially overlapping regions of the substrate, directly corresponding to instant claim 10.
Regarding instant claim 13, claim 22 of the ‘965 application teaches that the sensor comprises a single sensing element, directly corresponding to instant claim 13.
Regarding claim 14, claim 11 of the ‘965 application teaches that at least one polynucleotide sequence comprises the first polynucleotide sequence portion and the second polynucleotide sequence portion, directly corresponding to instant claim 14, wherein each polynucleotide molecule comprises one or more copies of both and the first and second polynucleotide sequence portions.
Regarding instant claim 15, claim 13 of the ‘965 application teaches that at least one first polynucleotide sequence comprises the first polynucleotide sequence portion and at least one second polynucleotide sequence comprises the second polynucleotide sequence portion, directly corresponding to instant claim 15, wherein the first and second polynucleotide sequence portions are respective portions of different polynucleotide molecules.
Regarding instant claim 20, claim 23 of the ‘965 application teaches that the first and second polynucleotide sequence portion are present in a cluster, directly corresponding to instant claim 20
Regarding instant claim 21, claim 24 of the ‘965 application teaches selecting the classification using a Gaussian mixture model, directly corresponding to instant claim 21.
Regarding instant claim 22, claim 8 of the ‘965 application teaches determining that the second polynucleotide sequence portion is modified relative to the first polynucleotide sequence portion at a location associated with the first and second nucleobases, directly corresponding to instant claim 22.
Any remaining limitations of instant claims 1-15 and 20-22 not expressly recited in the ‘965 application claims are rendered obvious by Shi as discussed in the 35 USC § 103 rejections above.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1-15 and 20-22 are provisionally rejected on the ground of
nonstatutory double patenting as being unpatentable over claims 1, 8, 16-21, and 32 of
copending Application No. 18/184,556 (US20230295719A1), in view of Shi (US8126235B2;
issued February 28th, 2012).
Although the claims at issue are not identical, they are not patentably distinct from each other because both the ‘556 and the instant application claim methods directed to the same core inventive concept of simultaneously sequencing two polynucleotide sequence portions co- localized within the same cluster on a substrate, detecting combined signals from both portions across two non-identical optical frequency ranges, and determining nucleobase identity based on the combined signal output.
Claim 1 of the ‘556 application teaches plurality of double stranded template polynucleotides on a substrate, contacting with first and second primers binding respectively to the first and second strand, extending both primers with labeled nucleobases, stimulating light emissions wherein the amplitude of the signal from the first labeled primers is greater than the amplitude from the second labeled primers, and identifying nucleobases based on the amplitude of the signal, establishing the physical sequencing framework and differential intensity required by the final wherein clause of instant claim 1. Claim 8 of the ‘556 application teaches contacting the first strand with unblocked first primers and contacting the second strand with a predetermined fraction of second primers, directly teaching the selective processing that produces the differential intensity required by step (d) of claim 1. Claim 16 of the ‘556 application detecting signals from both primer sets in two non-identical optical frequency ranges, directly corresponding to the first and second intensity data in non-identical optical frequency ranges of instant claims 1(a) and 1(b). Claim 32 of ‘556 application teaches receiving a first signal at a first amplitude and a second signal at a second amplitude and identifying nucleobases based on a combination of the first and second signals, directly corresponding to steps (a) through (d) of instant claim 1. The differential amplitude between the first and second labeled primers in claim 1 of the ‘556 application directly corresponds to step (d) of instant claim 1 requiring that the intensity of the signals based upon the first nucleobase is greater than the intensity based upon the second nucleobase.
The ‘556 application does not require at least one classification of the plurality of classifications represents more than one possible combination of respective first and second nucleobases, which is a limitation of instant claim 1 (c). Claim 20 of the ‘556 application recites sixteen classifications each representing a unique combination of nucleobase types, which is a classification framework that does not include a class covering more than one possible nucleobase combination.
However, Shi teaches this limitation, as discussed in the 35 USC § 103 rejections above. Shi teaches assigning membership to each of a plurality of intensity peaks by determining whether each peak belongs to none, the first DNA strand, the second DNA strand, or both the first DNA strand and the second, wherein the category where a peak belongs to both the first and second DNA strand explicitly represents a classification covering more than one possible nucleobase combination. Any combination of the first and second nucleobases that produces an overlapping co-occurring peak (claim 5). This teaching of Shi obviates the variation between the claims of ‘556 application and the instant application with the respect to the “at least one classification of the plurality of classifications represents more than one possible combination” limitation of claim 1c), rendering the claims of the instant application obvious over the claims of the ‘556 application in view of Shi. Any additional limitations of the claims of the instant application claims are encompassed by the open claim language “comprising” and are further rendered obvious by Shi as discussed in the 35 USC § 103 rejections above.
Regarding instant claim 2, claim 2 of the ‘556 application teaches identifying the labeled nucleobases added to the second primers are performed substantially simultaneously, directly corresponding to instant claim 2.
Regarding instant claim 3, claim 19 of the ‘556 application teaches identifying the labeled nucleobases is based on a combination of the extracted fluorescence intensities from the first and second fluorescent images, wherein the first and second fluorescent images correspond to the two non-identical optical frequency ranges established by claim 16 of the ‘556 application. This combined two-channel intensity basis for identification directly corresponds to the requirement of instant claim 3 that the classification is selected based on the combined intensity of the first and second signals and the combined of the third and fourth signals across the two optical channels.
Regarding instant claim 4, claim 20 of the ‘556 application teaches classifying a combination of identifies of labeled nucleobases as one of sixteen combinations based on a combination of extracted fluorescence intensities and predetermined fluorescence intensity distributions, directly corresponding to the sixteen-classification farmwork if instant claim 4.
Regarding instant claim 5, claim 21 of the ‘556 application teaches classifying based on predetermined normalized fluorescence intensity distributions, which corresponds to a predetermined number of classifications as recited in instant claim 5.
Regarding instant claim 6, claim 7 of the ‘556 application teaches that the amplitude of the signal generated by the second labeled primers corresponds with a second quantity of the second labeled primers in the cluster, establishing a quantitative relationship between the number of signal-capable primer populations and the resulting amplitude differential. This corresponds to the ratio limitation of instant claim 6. To the extent of the ‘556 application does not expressly recite the specific ration range of 1.25:1 to 5:1, Shi teaches an amplitude ration of approximately 2:1 between the major and minor traces (column 5, para 5 – column 6, para 1), rendering the specific ratio range of instant claim 6 obvious as discussed in the 35 USC § 103 rejections above.
Regarding instant claim 8, claim 1 of the ‘556 application teaches contacting with first and second primers, extending with labeled nucleobases to form first and second labeled primers, stimulating light emissions, and identifying nucleobases based on the amplitude of the signal, corresponds to the selective processing limitation underlying instant claim 8.
Regarding instant claims 9 and 10, claim 1 of the ‘556 application teaches contacting polynucleotides with first and second primers, extending with labeled nucleobases, and simulating light emissions, directly corresponding to the physical sequencing steps of instant claim 9 and 10.
Regarding instant claim 11, no claim of the ‘556 application directly recites spatially unresolved light emissions. Claim 3 of the ‘556 application establishes that signals from both primer population are emitted from the same region or substantially overlapping regions of the substrate, which implies spatial co-localization such that the signals are spatially unresolved at the detector. To the extent claim 3 of the ‘556 application does not expressly recite spatially unresolved emissions, Shi teaches that the function includes the superposition of information from both DNA strands (claim 4), which is inherently a spatially unresolved composite signal, rendering instant claim 11 obvious as discussed in the 35 USC § 103 rejections above.
Regarding instant claim 13, no claim of the ‘556 application directly recites a single sensing element. The single sensing element limitation is rendered obvious by Shi as discussed in the 35 USC § 103 rejections above.
Regarding instant claim 14, claim 5 of the ‘556 application teaches that the plurality of double stranded template polynucleotides in the cluster are generated by bridge amplification, establishing that each cluster contains copies of both the first strand and the second strand derived from the same original molecule, directly corresponding to instant claim 14 wherein each polynucleotide molecule comprises one or more copies of both the first and second polynucleotide sequence portions.
Regarding instant claim 15, claim 25 of the ‘556 application teaches hybridizing a first primer to a template polynucleotide and a second primer to the reverse complement of the template polynucleotide at substantially overlapping regions of a substrate, wherein the template polynucleotide and its reverse complement are distinct polynucleotide molecules, directly corresponding to instant claim 15 wherein the first and second polynucleotide sequence portions are respective portions of different polynucleotide molecules.
Regarding instant claim 20, claim 5 of the ‘556 application teaches that the plurality of double stranded template polynucleotides in the cluster are generated by a bridge amplification, and claim 6 of the ‘556 application teaches a plurality of clusters of nucleic acids, the clusters being randomly distributed on the substrate, directly corresponding to the cluster limitation of instant claim 20.
Regarding instant claim 21, claim 21 of the ‘556 application teaches classifying a combination of identities of labeled nucleobases as one of sixteen combinations based on normalized fluorescence intensities and predetermined normalized fluorescence intensity distributions, which is consistent with the Gaussian mixture model-based classification. To the extent claim 21 of the ‘556 application doesn’t explicitly recite the Gaussian mixture model, Shi teaches the probabilistic classification framework that would make the use of a Gaussian mixture model obvious, as discussed in the 35 USC § 103 rejection above.
Regarding instant claim 22, claim 25 of the ‘556 application teaches hybridizing a first primer to a template polynucleotide and a second primer to the reverse complement of the template polynucleotide at substantially overlapping regions of a substrate and determining the sequence of both by capturing combined light emissions. Differences between the sequence of the template and its reverse complements as determined by the classification output are indicative of sequence modifications, corresponding to the modification detection of instant claim 22. To the extent this correspondence is not direct, Shi renders this limitation obvious as discussed in the 35 USC § 103 rejection above.
Any remaining limitations of instant claims 1-15 and 20-22 not expressly recited in the ‘965 application claims are rendered obvious by Shi as discussed in the 35 USC § 103 rejections above.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
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/NURA M. CHOUDHURY/Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
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