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 .
Applicant’s arguments and amendments have been thoroughly reviewed and considered. Claims 4 and 11 have been canceled. Claims 16-32 remain withdrawn. Claim 33 has been added. Claims 1-3, 5-10, 12-15, and 33 are pending and are examined on the merits herein.
Response to Applicant’s Amendments
Information Disclosure Statement
In the Information Disclosure Statement submitted 7/25/2024, a foreign patent document (WO 2023/186819) was not considered because a copy was not provided. Applicant states in their Remarks that they have provided a copy of this foreign patent document, but no such document appears in the file wrapper. Additionally, if Applicant wishes for this document to be considered, they must file a new Information Disclosure Statement listing the foreign patent document. See MPEP 609.05(a). Thus, the foreign patent document remains not considered.
Claim Objections
Claim 15 was objected to due to a minor informality. In light of Applicant’s amendments to the claims submitted 2/5/2026, this objection has been withdrawn.
35 USC 112(a) Rejections
Claim 11 was rejected for reasons related to written description and enablement. Claim 11 has been canceled, and so this rejection has been rendered moot.
35 USC 112(b) Rejections
Claims 11 and 13-14 were rejected for various indefiniteness issues. In light of Applicant’s amendments to the claims submitted 2/5/2026, the rejections for claims 13 and 14 are withdrawn. Claim 11 has been canceled, and so this rejection has been rendered moot. See also new grounds of rejection below.
35 USC 103 Rejections
Claims 1-15 were rejected as being unpatentable over Romanov et al. (US 2018/0111957 A1) and various combinations of references. Claims 4 and 11 have been canceled, and so these rejections have been rendered moot.
Applicant’s arguments and amendments have been thoroughly reviewed and considered. These rejections have been maintained for all currently pending claims. See ”Response to Applicant’s Arguments” below. See also new grounds of rejection below for claim 33.
Response to Applicant’s Arguments
Regarding the 35 USC 103 Rejections presented in the Non-Final Rejection mailed 11/3/2025, Applicant argues that the rejections rely on impermissible hindsight using Applicant’s disclosure as a roadmap, and do not articulate any motivation or design principle that would lead the ordinary artisan to modify Romanov in the manner recited in the Non-Final Rejection (Remarks, pages 7-8). Applicant also argues that the reference does not teach all the features presented in claim 1, as the claim allegedly teaches that excitation at the first wavelength must occur twice, and the reference also allegedly does not teach that the third fluorescent dye is different from the first and second fluorescent dye as claimed (Remarks, pages 8-9). Finally, Applicant argues that the rejection does not consider claim 1 as a whole, particular with regard to the fact that the claim is directed to sequencing, and not simply the use of particular dyes (Remarks, page 9).
Regarding Applicant’s arguments that the Examiner has used impermissible hindsight, MPEP 2145 X (A) states, “Applicants may argue that the examiner’s conclusion of obviousness is based on improper hindsight reasoning. However, "[a]ny judgment on obviousness is in a sense necessarily a reconstruction based on hindsight reasoning, but so long as it takes into account only knowledge which was within the level of ordinary skill in the art at the time the claimed invention was made and does not include knowledge gleaned only from applicant’s disclosure, such a reconstruction is proper." In re McLaughlin, 443 F.2d 1392, 1395, 170 USPQ 209, 212 (CCPA 1971). "A factfinder should be aware, of course, of the distortion caused by hindsight bias and must be cautious of arguments reliant upon ex post reasoning. . . . Rigid preventative rules that deny factfinders recourse to common sense, however, are neither necessary under our case law nor consistent with it." KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 421, 82 USPQ2d 1385, 1397 (2007).” In the Non-Final Rejection, teachings from Applicant’s disclosure are not utilized (see para. 26 of the Non-Final Rejection). Teachings of Romanov were exclusively recited, and in combining elements of the reference, motivation was recited (see also para. 26 of the Non-Final Rejection, which states, “Thus, it would be prima facie obvious to have the first, second, and third nucleotides contain single fluorescent labels, where the third label is a long Stokes shift dye…This would allow the first and third labels to be excited at the same wavelength but be detected at different wavelengths (e.g. para. 10). The second and third labels could then be designed to have the same detection wavelengths, as this would limit the number of detection channels needed in the sequencing method/device overall, and would still allow discrimination of the three labels from one another, as the overall optical spectra would be different for each label (i.e. each label would have a distinct overall curve shape in a graph as shown in Figure 1 and explained in para. 118)…This design and method would cut down on the components needed in the device, which would decrease cost and improve efficiency.” Applicant does not appear to address these statements of motivation in their response.
Furthermore, MPEP 2145 X (A) notes that express motivation found within the reference is not required for a determination of obviousness, and MPEP 2141.03 I states, “‘A person of ordinary skill in the art is also a person of ordinary creativity, not an automaton.’ KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 421, 82 USPQ2d 1385, 1397 (2007). ‘[I]n many cases a person of ordinary skill will be able to fit the teachings of multiple patents together like pieces of a puzzle.’ Id. at 420, 82 USPQ2d 1397. Office personnel may also take into account ‘the inferences and creative steps that a person of ordinary skill in the art would employ.’ Id. at 418, 82 USPQ2d at 1396.” Therefore, the ordinary artisan would be capable of utilizing the various teachings of Romanov together to arrive at the claimed invention, even if said teachings are not explicitly recited in the same embodiment, utilizing ordinary creativity and knowledge generally available to one of ordinary skill in the art.
Regarding Applicant’s argument that the teachings of Romanov presented in the Non-Final Rejection do not teach all of the elements of claim 1, firstly, this is a reading of claim 1 too narrowly. MPEP 2111.01 II states, “…the court held that it was improper to read a specific order of steps into method claims where, as a matter of logic or grammar, the language of the method claims did not impose a specific order on the performance of the method steps, and the specification did not directly or implicitly require a particular order...” In Applicant’s arguments, they state that the claim requires excitation at the first excitation wavelength twice – once to detect the first labeled nucleotide and then later to detection the third labeled nucleotide. However, in the instant specification, though Figure 4 does describe a method in which the first excitation wavelength is explicitly used twice, this is not required in every embodiment of the instant specification. In fact, para. 92 states that all the labeled nucleotides may be delivered to the flow cell simultaneously, and thus the excitation at the first excitation wavelength would naturally affect the claimed first and third labeled nucleotides simultaneously in such a method. This interpretation of claim 1 is corroborated by instant claims 13 and 14, which state that the detection of the first and third fluorescent dyes may occur separately or simultaneously, respectively.
Furthermore, the sequencing described by Romanov encompasses sequential addition of a single nucleotide at a time to a polynucleotide, or the simultaneous use of 3 labeled nucleotides, followed by excitation and optical reading of the dye with emission filters (paras. 91-93). This would thus encompass detecting both the claimed first and third fluorescent dyes either one at a time or simultaneously, thus reading on multiple embodiments of claim 1. The rejection of claims 13 and 14 in the Non-Final Rejection also detail that sequential and simultaneous detection of the first and third dyes would be prima facie obvious given the teachings of Romanov, but Applicant does not appear to directly address these rejections.
Additionally, though Applicant states that Romanov does not teach that the third fluorescent dye may be different than the first and second fluorescent dyes, this is not accurate, as it is based on a singular paragraph of Romanov that is not indicative of all embodiments of the invention. Para. 93 alone states, “In particular embodiments each of the different nucleotide triphosphates (A, T, G and C) may be labelled with a unique fluorophore and also comprises a blocking group at the 3′ position to prevent uncontrolled polymerisation. Alternatively one of the four nucleotides may be unlabelled (dark),” thus detailing that at least three unique dyes may be used. Para. 110 also states the use of different dye compounds for each nucleotide, thus teachings the use of up to four distinct dyes.
Finally, regarding Applicant’s arguments that the 35 USC 103 Rejections do not consider the full sequencing method of the claims, the method of claim 1 requires exciting clusters of labeled polynucleotides, determining the clusters that did not produce fluorescent emissions, and using this to determine the sequence of the polynucleotides. As noted in the paragraphs above, Romanov teaches utilizing their dyes for a sequencing method where each individual labeled nucleotide can be identified, and where one label can be dark, and thus not emit any fluorescence. This is argued by the Examiner to read on the sequencing aspects of instant claim 1.
Therefore, Applicant’s arguments are not considered persuasive. In Applicant’s newly amended claims, the limitation of now canceled claim 4 has been incorporated into claim 1. As previous claim 4 was rejected in the initial teachings of Romanov described in the 35 USC 103 Rejections of the Non-Final Rejection, and these teachings also read on newly amended claim 1, the rationale for rejecting the newly amended claims remains the same, and so these rejections have been maintained. As claim 33 is newly added, it required the new grounds of rejection presented below.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 112(a) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application No. 63/325,057, fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application. Specifically, this application does not describe any of the dyes recited in instant claims 9-10. Therefore, these claims will receive an effective filing date that is the filing date of the instant application, 3/27/2023.
Claim Rejections - 35 USC § 112(b)
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.
Claim 33 is 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 33 recites “sequencing of the clusters,” which is not a step that is recited in claims 1 or 3, from which this claim depends. Claim 1 recites “determining the sequence of the polynucleotides” where the polynucleotides are in clusters, but this is more narrow in scope than sequencing the clusters, as the individual polynucleotides of the clusters may have different nucleotide sequences. It is therefore unclear if Applicant intended for these two sequencing recitations to be analogous. The claim will be interpreted as though it is referring to the determining step recited in claim 1, but it is recommended that Applicant amend claim 33 to more closely align with the language of claim 1, or amend the final determining step of claim 1 to be in line with the language of claim 33.
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 1-3, 6, 10, 13-14, and 33 are rejected under 35 U.S.C. 103 as being unpatentable over Romanov et al. (US 2018/0111957 A1).
Romanov teaches fluorescent labels for nucleotides with applications for sequencing (Abstract). Their methods can be used to sequence template polynucleotides on clustered arrays utilizing modified nucleotides labeled with dye compounds (paras. 100-101). The excitation wavelength of any two dyes may be different from one another (paras. 47 and 110; instant claim 2). The emission wavelengths for any two labels can also be different (para. 46; instant claim 3). Romanov teaches that more than two labels can be used (para. 46). Three nucleotides can each be labeled with a unique fluorescent dye compounds, while the fourth dye can remain dark (para. 110). The A, T, G, and C dNTPs can use this unique labeling method during sequencing, where excitation may occur and then emission spectra are detected (paras. 92-93). The labels can include a dye that contains a Stokes shift, and particularly dyes with a long Stokes shift (paras. 48 and 50). The Stokes shift dyes of Romanov have shifts greater than 50 nm, overlapping with the range described in instant claim 6. Thus, it would be prima facie obvious to have the first, second, and third nucleotides contain single fluorescent labels, where the third label is a long Stokes shift dye. This would allow the first and third labels to be excited at the same wavelength but be detected at different wavelengths (e.g. para. 10). The second and third labels could then be designed to have the same detection wavelengths, as this would limit the number of detection channels needed in the sequencing method/device overall, and would still allow discrimination of the three labels from one another, as the overall optical spectra would be different for each label (i.e. each label would have a distinct overall curve shape in a graph as shown in Figure 1 and explained in para. 118). Taking this dye construction together with the sequencing described above would lead to the method described by instant claim 1. This design and method would cut down on the components needed in the device, which would decrease cost and improve efficiency.
Regarding claim 10, Romanov teaches the use of NR550S0 as a dye (paras. 118-119 and Figures 1-2), along with teaching the structure of the molecule between paras. 139 and 140. It is also shown as being compared with other dyes, where emission spectra can be distinguished between it and NR5201s (Figures 1 and 2). It would be prima facie obvious to use a dye described and used by Romanov in the invention of Romanov, particularly if its fluorescent spectra is not identical to a similar dye such as NR5201s. As noted above, the method of Romanov used in the rejection of claim 1 utilizes three different dyes for the first three labeled nucleotides. There are not particular requirements for the first two dyes in the method of Romanov, so long as they are distinguishable from one another. The ordinary artisan would thus recognize that NR550S0 could operate as the first or second nucleotide label in the method of Romanov described above, with no change to the overall method other than the choosing of other dyes meeting the requirements of instant claim 1. As Romanov teaches many types of dyes (e.g. paras. 12-16), this would be possible for the ordinary artisan, and so it would be prima facie obvious to include NR550S0 as the first or second nucleotide label.
Regarding claim 13, Romanov notes that for sequencing-by-synthesis methods that may be used with the dyes of the invention, nucleotides may be added sequentially to the strand complementary to the template nucleic acid being sequenced (para. 91). In the embodiment of Romanov described in the rejection of claim 1 above, the first and third labels are excited at the same wavelength but detected at different wavelengths. When combining this teaching with sequencing-by-synthesis methods, it would still be prima facie obvious to add each nucleotide sequentially and separately, thereby meeting the limitations of instant claim 13. This would ensure that sequencing data is as accurate as possible, and that only a single type of nucleotide is incorporated into the complementary strands at one time. If multiple nucleotides are added to the array at once, multiple nucleotides may be incorporated into a single strand at the same time, which could lead to missed base incorporations within the sequencing data.
Regarding claim 14, Romanov teaches that when using Stokes shift dyes, a single excitation wavelength can be used with a range of detection wavelength measurements, so as to pick up emission wavelengths from two dyes (para. 10). The reference also discusses being able to tell different dyes apart through optical distinguishing (paras. 47 , 110, and 119). Because in the embodiment of Romanov described in the rejection of claim 1 above, the first and third labels are excited at the same wavelength but detected at different wavelengths, it would be prima facie obvious to detect these signals simultaneously on the clustered array. This would mean that two labeled nucleotides can be used for sequencing simultaneously, but could still be distinguished from one another in the optical data due to Stokes shifts. By taking advantage of these detection properties, sequencing of multiple different clusters of sequences could occur faster, as not every nucleotide would need to be introduced to the array individually. There would be a reasonable expectation of success as this would not change the sequencing analysis, it would just alter the way the nucleotides are introduced to the array.
Regarding claim 33, in the teachings of Romanov described above in the rejection of claim 1, three different fluorescent dyes are used, where the third dye is a long Stokes shift dye. This third dye has the same emission wavelength as the second dye, while the first dye has its own emission wavelength. This three-dye method is capable of use in sequencing with a fourth unlabeled nucleotide. Romanov teaches that when two dyes have the same emission wavelength, they may be detected with the same emission channel during sequencing, which cuts down on the complexity of the sequencing device as less emission filters are needed (paras. 10-11 and 53). Para. 142 of the reference notes that traditional sequencing platforms may use four detection channels. Thus, given the teachings of Romanov described above, it would be prima facie obvious that the device required to perform sequencing with the three different fluorescent dyes described above would require two detection channels – one for the first dye and one for the second and third dye, based on their emission wavelengths. The unlabeled nucleotide would not require a detection channel. This would still cut down on the traditional number of detection channels needed for sequencing from four to two, thus allowing for a less complex device to be used, which may lower sequencing error and noise. This setup would also allow the dyes to still function as intended, thus maintaining the benefits of the use of the dyes described above in the rejection of claim 1. As Romanov teaches such detection channels, and that the use of multiple detection channels is already known in the art, there would be a reasonable expectation of success in utilizing such a sequencing device.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Romanov et al. (US 2018/0111957 A1) in view of Bergren et al. (US 2017/0261313 A1).
Romanov teaches the methods of claims 1-3, 6, 10, 13-14, and 33, as described above. Though the reference does provide many teachings about long Stokes shift dyes, it does not specify that the long Stokes shift dye may have a shift ranging from about 300 meV to 850 meV.
Bergren teaches a fluorescent liquid penetrant (Abstract). Specifically, the liquid can contain fluorophores that have a Stokes shift of more than 300 meV or more than 400 meV (para. 73).
MPEP 2144.05 I states, “In the case where the claimed ranges "overlap or lie inside ranges disclosed by the prior art" a prima facie case of obviousness exists. In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976); In re Woodruff, 919 F.2d 1575, 16 USPQ2d 1934 (Fed. Cir. 1990)… Similarly, a prima facie case of obviousness exists where the claimed ranges or amounts do not overlap with the prior art but are merely close. Titanium Metals Corp. of America v. Banner, 778 F.2d 775, 783, 227 USPQ 773, 779 (Fed. Cir. 1985).” Applicant has not provided evidence that the energy range recited in claim 5 is critical, as the instant specification simply mentions the same limitation as the instant claim (para. 118). In light of the teachings of Romanov, which recite long Stokes shift dyes and Bergren, which recite said dyes with a shift in the claimed range, the energy range recited in claim 5 is considered routine optimization, and the specific claimed parameters are not viewed as inventive.
Thus, claim 5 is prima facie obvious over Romanov in view of Bergren.
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Romanov et al. (US 2018/0111957 A1) in view of Lopez et al. (US 2015/0316543 A1).
Romanov teaches the methods of claims 1-3, 6, 10, 13-14, and 33, as described above. Though the reference does provide many teachings about long Stokes shift dyes, it does not specify that the long Stokes shift dye may be excited at about 300 nm.
Lopez teaches luminescent complexes for detection of compounds (Abstract). The reference teaches that it is possible to have a long Stokes shift dye that is excited at 300 nm, where the emission wavelength is 600 nm and the Stokes shift is 300 nm (para. 83).
Romanov teaches that with long Stokes shift dyes, detection emissions may be between 550-570 nm (para. 10), and that Stokes shifts may be greater than 150 nm (para. 42) Thus, prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to substitute a long Stokes shift dye such as the one described by Lopez for the third labeled nucleotide in the invention of Romanov, as said dye would overlap with the teachings of long Stokes shift dyes of Romanov. MPEP 2143 I (B) states, “The rationale to support a conclusion that the claim would have been obvious is that the substitution of one known element for another yields predictable results to one of ordinary skill in the art.” The teachings of Lopez would provide the ordinary artisan with evidence that such a long Stokes shift dye could be obtained and used for fluorescence detection, and as fluorescence dyes are well known in the art, as evidenced by Lopez and Romanov, the results of using such dyes would be predictable.
Thus, claim 7 is prima facie obvious over Romanov in view of Lopez.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Romanov et al. (US 2018/0111957 A1) in view of Liu et al. (Chem. Commun., 2018).
Romanov teaches the methods of claims 1-3, 6, 10, 13-14, and 33, as described above. However, the reference does not teach the use of a chromenoquinoline dye.
Liu teaches the use of chromenoquinoline dyes for staining cellular components (Abstract). Depending on the specific dye used, a variety of fluorescence spectra can be obtained (Figure 2). Particular chromenoquinoline dyes also showed large Stokes shifts, which are taught to be beneficial for fluorescent microscopy (page 1510, column 1, para. 3). Generally, Liu teaches that these dyes can have “relatively high quantum yields, large absorption extinction coefficients, large Stokes shifts and good water solubility,” (page 1511, column 2, para. 4).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to substitute a chromenoquinoline dye into the method of Romanov as the third labeled nucleotide, as this nucleotide is already described as a long Stokes shift dye. MPEP 2143 I (B) states, “The rationale to support a conclusion that the claim would have been obvious is that the substitution of one known element for another yields predictable results to one of ordinary skill in the art.” Chromenoquinoline dyes are known and can be used in fluorescent detection methods, as evidenced by Liu, and as their emission spectra are known, it would be possible to use them in sequencing methods. Utilizing this dye in Romanov, which already teaches the use of long Stokes shift dyes, would produce similar results to the methods of Romanov alone, as the chromenoquinoline would be capable of detection and discrimination from other dyes. As noted above, the method of Romanov used in the rejection of claim 1 above utilizes three different dyes for the first three labeled nucleotides, where the third dye is a long Stokes shift dye. There are no other particular requirements for the three dyes, so long as they are distinguishable from one another. The ordinary artisan would thus recognize that a chromenoquinoline dye could operate as the third nucleotide label with no change to the overall method other than the choosing of other dyes that meet the requirements of instant claim 1. As Romanov teaches many types of dyes (e.g. paras. 12-16), this would be possible for the ordinary artisan, and so it would be prima facie obvious to use a chromenoquinoline dye as the third nucleotide label.
Thus, claim 8 is prima facie obvious over Romanov in view of Liu.
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Romanov et al. (US 2018/0111957 A1), hereby called Romanov 1, in view of Romanov et al. (CA 3,114,733 A1), hereby called Romanov 2.
Romanov 1 teaches the methods of claims 1-3, 6, 10, 13-14, and 33, as described above. However, the reference does not teach the use of NR455BoC as a dye or label.
Romanov 2 teaches detection of fluorescent dyes in the context of labeled nucleotides (Abstract). The reference teaches the use of NR455BoC in exemplary dye sets (see the table at the top of page 108), teaches the structure of an NR455BoC dye (see the figure before the table of page 108), and shows the successful detection of this dye in Figures 9-11 and 13. Particularly, it is noted that NR455BoC can be used in sequencing methods that detect all four nucleotides, can be used in multiplex imaging methods (paras. 18-19 and 21), and can be used in methods where a fourth nucleotide is unlabeled (para. 334).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to substitute NR455BoC into the method of Romanov 1 as one of the first two labeled nucleotides. MPEP 2143 I (B) states, “The rationale to support a conclusion that the claim would have been obvious is that the substitution of one known element for another yields predictable results to one of ordinary skill in the art.” NR455BoC is a known dye for use in nucleotide fluorescent detection methods, as evidenced by Romanov 2, and its use in sequencing methods to produce detectable and categorizable emission spectra is known. Utilizing this dye in Romanov 1 would produce the similar results to the methods of Romanov 1 alone, as the methods of Romanov 1 and Romanov 2 are very similar. As noted above, the method of Romanov 1 used in the rejection of claim 1 above utilizes three different dyes for the first three labeled nucleotides. There are no particular requirements for the first two dyes, so long as they are distinguishable from one another. The ordinary artisan would thus recognize that NR455BoC could operate as either the first or second nucleotide label with no change to the overall method other than the choosing of other dyes the meet the requirements of instant claim 1. As Romanov 1 teaches many types of dyes (e.g. paras. 12-16), this would be possible for the ordinary artisan, and so it would be prima facie obvious to use NR455BoC as either the first or second nucleotide label.
Thus, claim 9 is prima facie obvious over Romanov 1 in view of Romanov 2.
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over Romanov et al. (US 2018/0111957 A1), in view of Langlois et al. (US 2020/0080142 A1).
Romanov teaches the methods of claims 1-3, 6, 10, 13-14, and 33, as described above. Though the reference also teaches charge-coupled devices generally for detecting fluorescent signals (para. 93), the reference does not teach that the first and second detection wavelengths may be detected with separate charge-coupled devices.
Langlois teaches sequencing methods involving light sources and detectors (Abstract). The sequencing methods can include an optics system for capturing fluorescent images (e.g. para. 21). The optics system can include a detector, such as a charge-coupled device sensor (para. 23). The optics system can also include two detectors, where each detector operates at a particular wavelength (para. 25). This can allow simultaneous detection of two wavelengths, which can speed up the imaging process (para. 25).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Langlois in the method of Romanov, and specifically, to provide two charge-coupled devices to detect the first and second detection wavelengths of Romanov. Langlois teaches that the use of two detection wavelength can provide faster imaging and allow for simultaneous detection, which would cut down on sequencing time, making for an overall more efficient process and motivating the ordinary artisan. There would be a reasonable expectation of success because Romanov already teaches that charge-coupled detection devices can be used in their methods, and the charge-coupled devices of Langlois are used in a similar context and have the same function as those of Romanov.
Thus, claim 12 is prima facie obvious over Romanov in view of Langlois.
Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Romanov et al. (US 2018/0111957 A1) in view of Sun et al. (US 2018/0258468 A1).
Romanov teaches the methods of claims 1-3, 6, 10, 13-14, and 33, as described above. However, this reference does not teach the use of a time delay imaging system for detecting the nucleotide labels.
Sun teaches imaging systems associated with samples (Abstract). Specifically, the reference teaches imaging systems in relation to sequencing, and teaches optical sequencers that incorporate time delay integration to detect fluorescence emissions (paras. 2-3). Such an imaging system can be used with light beams hitting a sample, where said sample can be on a an array (para. 6-9 and 69). This type of imaging can enable high throughput scanning of fluorescence emissions (para. 3).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to utilize the time delay integration taught by Sun in the method of Romanov to detect the labeled nucleotides. Romanov teaches the use of arrays and light excitation sources (e.g. paras. 46 and 100-101), and also notes sequencing methods (Abstract), similar to the teachings of Sun. Romanov teaches that the particular base added to a sequence can be determined in an imaging step (para. 91), and generally teaches imaging devices (para. 102), but does not provide specifics on the structure or use of these devices. Thus, the time delay integration of Sun could act as a simple substitution for the imaging methods of Romanov. MPEP 2143 I (B) states, “The rationale to support a conclusion that the claim would have been obvious is that the substitution of one known element for another yields predictable results to one of ordinary skill in the art.” The use of time delay integration was known, as evidenced by Sun, and could be successfully and predictably used in sequencing methods to detect fluorescent emissions, providing evidence of predictable results in the method of Romanov.
Thus, claim 15 is prima facie obvious over Romanov in view of Sun.
Conclusion
No claims are currently allowable.
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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/F.F.G./Examiner, Art Unit 1681
/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681