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 .
Priority
Receipt is acknowledged of papers submitted under 35 U.S.C. 119(a)-(d), which papers have been placed of record in the file.
Status of Claims
Claims 1, 9, 11, 13, 15-16, 19, 22, 29-30, 35-40, 42, 80, 159, 238 and 239 are pending in this application.
35 USC § 101 Statutory Analysis
The claims do not recite any of the judicial exceptions enumerated in the 2019 Revised Patent Subject Matter Eligibility Guidance. Further, the claims do not recite any method of organizing human activity, such as a fundamental economic concept or managing interactions between people. Finally, the claims do not recite a mathematical relationship, formula, or calculation. Thus, the claims are eligible because they do not recite a judicial exception.
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 claims at issue 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); and 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 a nonstatutory double patenting ground provided the reference application or patent either is shown to be commonly owned with this 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 §§ 706.02(l)(1) - 706.02(l)(3) 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).
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Claims 1, 9, 11, 13, 15-16, 19, 22, 29-30, 35-40, 42, 80, 159, 238 and 239 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 6, 9, 18, 21-24, 32-34, 43, 49, 55, 67, 88, 133, 182 and 188 of copending U.S. Patent Application No. 19/170,863. Although the conflicting claims are not identical, they are not patentably distinct from each other because both sets of claims are directed towards the common subject matter.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
The claims in the present application define the invention differently from the claims in copending U.S. Patent Application No. 19/170,863, however they are not patentably distinguishable from the claims in the other copending application. In re White et al., 160 USPQ 417, In re Thorington et al., 163 USPQ 644.
For example, comparing representative claim 1 of the present application with representative claim 43 of copending U.S. Patent Application No. 19/170,863. Claim 1 of the present application recites: A method for phasing and prephasing correction in sequencing analysis, comprising (Claim 43 of copending U.S. Patent Application No. 19/170,863 recites: A computer-implemented method for base calling in sequencing data analysis, comprising); determining, by a processor, corrected image intensities of a plurality ofpolonies of flow cell images in a cycle N, Ipc(N), and optionally in a cycle N+1, Ipc(N+1), based on a cycle N-1 phasing coefficient, pN-1, a cycle N-1 prephasing coefficient, ppN-1, or both the cycle N-1 phasing coefficient and the cycle N-1 prephasing coefficient of the plurality of polonies from a cycle N-1 (Claim 43 of copending U.S. Patent Application No. 19/170,863 recites: obtaining, by a processor, a plurality of flow cell images … performing one or more primary analysis steps to adjust image intensities of polonies in the first MIP image or the one or more MIP images); obtaining, by the processor, base calls in the cycle N based on the corrected image intensities of the plurality of polonies in the cycle N, Ipc(N) (Claim 43 of copending U.S. Patent Application No. 19/170,863 recites: making base calls for the polonies based on the adjusted image intensities); selecting, by the processor, a set of polonies from the plurality of polonies based on the base calls in the cycle N based on the base calls in the cycle N (Claim 43 of copending U.S. Patent Application No. 19/170,863 recites: performing one or more primary analysis steps to adjust image intensities of polonies in the first MIP image or the one or more MIP images; and making base calls for the polonies based on the adjusted image intensities); determining, by the processor, a cycle N phasing coefficient, pN, a cycle N prephasing coefficient, ppN, or both the cycle N phasing coefficient and the cycle N prephasing coefficient based on image intensities of the set of selected polonies for the cycle N (Claim 43 of copending U.S. Patent Application No. 19/170,863 recites: wherein the one or more primary analysis steps comprises … intensity offset adjustment … intensity normalization … phasing and prephasing correction); and updating, by the processor, image intensities of the plurality of polonies in cycle N, I(N), using updated and corrected image intensities, (N), wherein (N) is obtained based on the cycle N phasing coefficient, pN, the cycle N prephasing coefficient, ppN, or both (Claim 43 of copending U.S. Patent Application No. 19/170,863 recites: wherein performing base callings using the first MIP image comprises performing one or more primary analysis steps to adjust image intensities of polonies in the first MIP image or the one or more MIP images; and making base calls for the polonies based on the adjusted image intensities, wherein the one or more primary analysis steps comprises, background subtraction, image sharpening, intensity offset adjustment, color correction, intensity normalization, phasing and prephasing correction, image registration, quality score estimation or a combination thereof).
As the comparison shows the claims recite common subject matter, and the differences relate to variations of the claimed limitations, and the processing is carried out on the data and/or elements in no way affects how the data would be received from an input, processed and output within the context of the claims. Therefore, the substitution of the different variations would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention. While claim 43 of copending U.S. Patent Application No. 19/170,863 includes additional limitations that are not set forth in the instant claim 1, the use of transitional term "comprising" in the instant claim 1 fails to preclude the possibility of additional elements, so that instant claim 1 fails to define an invention that is patentably distinct from claim 43 of copending U.S. Patent Application No. 19/170,863. Furthermore, the elements of instant claim 1 are fully anticipated by the claim in the copending application, and anticipation is “the ultimate or epitome of obviousness (In re Kalm, 154 USPQ 10 (CCPA 1967), also In re Dailey, 178 USPQ 293 (CCPA 1973) and In re Pearson, 181 USPQ 641 (CCPA 1974)).
Claims 9, 11, 13, 15-16, 19, 22, 29-30, 35-40, 42, 80, 159, 238 and 239 of the present application recite limitations which are in most cases word for word the same limitations as found in claims 1, 3, 6, 9, 18, 21-24, 32-34, 49, 55, 67, 88, 133, 182 and 188 respectively of copending U.S. Patent Application No. 19/170,863.
Claim Rejections - 35 USC § 102
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 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 the appropriate paragraphs of 35 U.S.C. §102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1, 9, 11, 13, 15-16, 19, 22, 29-30, 35-36, 38-40, 42, 80, 159, 238 and 239 are rejected under 35 U.S.C. §102(a)(1) as being anticipated by Garcia et al. (U.S. Patent No. US 8,965,076 B2) (hereafter referred to as “Garcia”).
With regard to claim 1, Garcia describes determining, by a processor (see Figure 1, element 26 and refer for example to paragraph [0111]), corrected image intensities of a plurality of polonies of flow cell images in a cycle N, Ipc(N), based on a cycle N-1 phasing coefficient, pN-1, a cycle N-1 prephasing coefficient, ppN-1, or both the cycle N-1 phasing coefficient and the cycle N-1 prephasing coefficient of the plurality of polonies from a cycle N-1 (see Figure 3, element 224 and refer for example to paragraphs [0127) and [0128]); obtaining, by the processor (see Figure 1, element 26 and refer for example to paragraph [0111]), base calls in the cycle N based on the corrected image intensities of the plurality of polonies in the cycle N, Ipc(N) (see Figure 3, element 224 and refer for example to paragraphs [0127] and [0128]); selecting, by the processor (see Figure 1, element 26 and refer for example to paragraph [0111]), a set of polonies from the plurality of polonies based on the base calls in the cycle N based on the base calls in the cycle N (see Figure 3, element 226 and refer for example to paragraph [0108], [0109], [0110], [0127] and [0128]); determining, by the processor (see Figure 1, element 26 and refer for example to paragraph [0111]), a cycle N phasing coefficient, pN, a cycle N prephasing coefficient, ppN, or both the cycle N phasing coefficient and the cycle N prephasing coefficient based on image intensities of the set of selected polonies for the cycle N (see Figure 3, element 224 and refer for example to paragraphs [0108] and [0128]); and updating, by the processor (see Figure 1, element 26 and refer for example to paragraph [0111]), image intensities of the plurality of polonies in cycle N, I(N), using updated and corrected image intensities, (N), wherein (N) is obtained based on the cycle N phasing coefficient, pN, the cycle N prephasing coefficient, ppN, or both (see Figure 3, element 224 and refer for example to paragraphs [0127] and [0128]).
As to claim 9, Garcia describes determining updated and corrected image (N), based on the cycle N phasing coefficient, pN, the cycle N prephasing coefficient, ppN, or both (see Figure 3, element 224 and refer for example to paragraph [0108], [0109], [0110], [0127] and [0128]).
In regard to claim 11, Garcia describes generating normalized image intensities, Inorm(N), by normalizing the corrected image intensities in cycle N, Ipc(N) (see Figure 3, element 224 and refer for example to paragraph [0065] and [0128]).
With regard to claim 13, Garcia describes generating normalized image intensities, Inorm(N+1), by normalizing the corrected image intensities in cycle N+1, Ipc(N+1) (see Figure 3, element 224 and example to paragraph [0065] and [0128]).
As to claim 15, Garcia describes updating the normalized image intensities, Inorm(N) using corrected normalized image intensities, Inorm_n(N) (see Figure 3, element 224 and refer for example to paragraph [0065] and [0128]).
In regard to claim 18, Garcia describes wherein determining the corrected image intensities in cycle N, Ipc(N), is further based on the image intensities of the plurality of polonies in cycle N, I(N) (see Figure 3, element 224 and refer for example to paragraphs [0127] and [0128]).
With regard to claim 21, Garcia describes wherein the determining the corrected image intensities in cycle N+1, Ipc(N+1), is further based on image intensities of the plurality of polonies in cycle N+1, I(N+1) (see Figure 3, element 224 and refer for example to paragraphs [0127] and [0128]).
As to claim 29, Garcia describes making, by the processor (see Figure 1, element 26 and refer for example to paragraph [0111]), the base calls in the cycle N+1 using the corrected image intensities of the plurality of polonies in the cycle N+1, Ipc(N+1) (see Figure 3, elements 224 and 226, and refer for example to paragraphs [0108], [0109], [0110], [0127] and [0128]).
In regard to claim 30, Garcia describes wherein obtaining the base calls in the cycle N based on the corrected image intensities of the plurality of polonies in the cycle N, Ipc(N) comprises making the base calls using the corrected image intensities of the plurality of polonies in the cycle N, Ipc(N), by identifying nucleotide bases corresponding to the plurality of polonies in the cycle (see Figure 3, elements 224 and 226, and refer for example to paragraphs [0108], [0109], [0110], [0127] and [0128]).
With regard to claim 35, Garcia describes wherein selecting the set of polonies from the plurality of polonies comprises for each channel of one or more channels selecting polonies that are called a base corresponding to the channel in the cycle N and called a different base in the cycle N-1, selecting polonies that are called a base corresponding to the channel in the cycle N and called a different base in cycle N+1 or a combination thereof (refer for example to paragraphs [0392] and [0416]).
As to claim 36, Garcia describes fitting the image intensities of the set of selected polonies using one or two linear functions (refer for example to paragraphs [0104], [0223], [0392] and [0416]).
With regard to claim 38, Garcia describes for each channel of one or more channels, generating corrected normalized image intensities, In or n(N), based on image intensities of polonies that are called a base corresponding to the channel, and updating a normalized image intensity, Inorm_(N), by using the corrected normalized image intensities, Inorm_n(N) (see Figure 3, element 224 and refer for example to paragraphs [0065], [0016] and [0128]).
As to claim 39, Garcia describes wherein the generating the corrected normalized image intensities, Inor (N), based on the image intensities of the polonies that are called a base corresponding to the channel comprises determining a normalization factor using the image intensities of the polonies that are called the base corresponding to the channel (see Figure 3, element 224 and refer for example to paragraphs [0065], [0016] and [0128]).
In regard to claim 40, Garcia describes wherein the normalization factor is an image intensity selected from a range of intensity among at least part of the polonies that are called the base corresponding to the channel (see Figure 3, element 224 and refer for example to paragraphs [0065], [0016] and [0128]).
With regard to claim 42, Garcia describes updating the base calls of the cycle N based on the updated normalized image intensities, Inorm(N) (see Figure 3, element 224 and refer for example to paragraphs [0065] and [0128]).
As to claim 80, Garcia describes determining, by a processor (see Figure 1, element 26 and refer for example to paragraph [0111]), a cycle N-1 phasing coefficient, pN-1, a cycle N-1 prephasing coefficient, ppN-1, or both the cycle N-1 phasing coefficient and the cycle N- 1 prephasing coefficient of a plurality of polonies of flow cell images in a cycle N-1 (see Figure 3, element 224 and refer for example to paragraphs [0127) and [0128]); determining, by the processor, corrected image intensities of the plurality of polonies in a cycle N, Ipc(N), based on the cycle N-1 phasing coefficient, pN-1, the cycle N-1 prephasing coefficient, ppN-1, and image intensities of the plurality of polonies in the cycle N, I(N) (see Figure 3, element 224 and refer for example to paragraphs [0127) and [0128]); and iterating, by a processor, until a stopping criteria is met, one or more of: determining, by the processor (see Figure 1, element 26 and refer for example to paragraph [0111]), corrected image intensities of the plurality of polonies in a cycle N+1, Ipc(N+1), based on the cycle N-1 phasing coefficient, pN-1; the cycle N-1 prephasing coefficient, ppN- 1 (see Figure 3, element 224 and refer for example to paragraphs [0127) and [0128]); and the image intensities of the plurality of polonies in the cycle N, I(N) in response to determining that a cycle N phasing coefficient, pN, and a cycle N prephasing coefficient, ppN, are not available or the cycle N phasing coefficient, pN, the cycle N prephasing coefficient, ppN v (see Figure 3, element 224 and refer for example to paragraphs [0127) and [0128]); and the image intensities of the plurality of polonies in the cycle N, I(N), or image intensities of the plurality of polonies in the cycle N+1,I(N+1), in response to determine that the cycle N phasing coefficient, pN, and the cycle N prephasing coefficient, ppN, are available (see Figure 3, element 224 and refer for example to paragraphs [0127) and [0128]); obtaining, by the processor (see Figure 1, element 26 and refer for example to paragraph [0111]), base calls in the cycle N based on the corrected image intensities of the plurality of polonies in the cycle N, Ipc(N) (see Figure 3, element 224 and refer for example to paragraphs [0127] and [0128]); selecting, by the processor (see Figure 1, element 26 and refer for example to paragraph [0111]), a set of polonies from the plurality of polonies based on the base calls in the cycle N (see Figure 3, element 226 and refer for example to paragraph [0108], [0109], [0110], [0127] and [0128]) ; determining, by the processor (see Figure 1, element 26 and refer for example to paragraph [0111]), the cycle N phasing coefficient, pN, and the cycle N prephasing coefficient, ppN, based on the image intensities of the set of selected polonies (see Figure 3, element 224 and refer for example to paragraphs [0108] and [0128]); and updating, by the processor (see Figure 1, element 26 and refer for example to paragraph [0111]), the image intensities of the plurality of polonies in cycle N, I(N), using updated and corrected image intensities, Ipc n(N), wherein Ipc n(N) is obtained based on the cycle N phasing coefficient, pN, and the cycle N prephasing coefficient, ppN (see Figure 3, element 224 and refer to paragraphs [0127] and [0128]).
In regard to claim 159, Garcia describes generating, by a sequencing system, flow cell images by conducting one or more cycles of sequencing reactions of a plurality of nucleic acid template molecules immobilized on a support, wherein the flow cell image comprises a plurality of polonies corresponding to the plurality of nucleic acid template molecules (see Figure 3, element 224 and refer for example to paragraphs [0127) and [0128]); selecting, by a processor (see Figure 1, element 26 and refer for example to paragraph [0111]), a subset of polonies from the plurality of polonies ; determining, by the processor, a cycle N phasing coefficient, pN, or a cycle N prephasing coefficient, ppN, that maximizes a quality or purity of image intensities of the set of selected polonies in the cycle N and is based on a penalty function (see Figure 3, element 226 and refer for example to paragraph [0108], [0109], [0110], [0127] and [0128]); updating, by the processor (see Figure 1, element 26 and refer for example to paragraph [0111]), image intensities of the plurality of polonies in cycle N,I(N), using updated and corrected image intensities, I(N), wherein i(N) is obtained based on the cycle N phasing coefficient, pN, the cycle N prephasing coefficient, ppN, or both; and performing, by the processor (see Figure 3, element 224 and refer for example to paragraphs [0127] and [0128]), base calling of the plurality of polonies using the updated image intensities of the plurality of polonies, I(N), in cycle N (see Figure 3, element 224 and refer for example to paragraphs [0127] and [0128]).
With regard to claim 238, Garcia describes generating, by a sequencing system, the flow cell images by conducting one or more cycles of sequencing reactions of a plurality of nucleic acid template molecules immobilized on a support, wherein the flow cell image comprises image intensities of the plurality of polonies corresponding to the plurality of nucleic acid template molecules in one or more samples, and wherein the one or more cycles comprises the cycle N and the cycle N-1 (refer for example to paragraphs [0001] through [0004], and to paragraphs [0127) and [0128]).
As to claim 239, Garcia describes generating, by a sequencing system, the flow cell images from one or more cellular sample(s) by conducting one or more cycles of sequencing reactions of a plurality of concatemer molecules of the one or more cellular sample(s) immobilized on a support, wherein the flow cell images comprise image intensities of the plurality of polonies corresponding to the plurality of concatemer molecules in the one or more samples, and wherein the one or more cycles comprises the cycle N and the cycle N-1 (refer for example to paragraphs [0001] through [0004], and to paragraphs [0127], [0128] and [0430], and refer for example to the right side of page 44 which shows various complete genomes).
Allowable Subject Matter
Claims 37 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Relevant Prior Art
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Langlois, Hunter and Karunakaran all disclose systems similar to applicant’s claimed invention.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jose L. Couso whose telephone number is (571) 272-7388. The examiner can normally be reached on Monday through Friday from 5:30am to 1:30pm.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Matthew Bella, can be reached on 571-272-7778. The fax phone number for the organization where this application or proceeding is assigned is (571) 273-8300.
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/JOSE L COUSO/Primary Examiner, Art Unit 2667
July 14, 2026
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