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 1-20 are pending and are examined on the merits herein.
Response to Applicant’s Amendments and Arguments
Drawings Objections
The drawings were objected to because they included reference signs not mentioned in the description and because Figures 10 and 11 contained typographical errors. Applicant has provided newly amended copies of Figures 10 and 11 to overcome this latter objection. However, Applicant does not appear to have addressed the rejection regarding reference signs not mentioned in the description, as no substitute specification or amended Figure 6 has been included in Applicant’s response, and Applicant’s reply makes no remarks regarding this objection. Therefore, these objections have been maintained-in-part.
Claim Objections
Claims 13-14, 17-18, and 20 were objected to due to minor informalities. In light of Applicant’s amendments to the claims submitted 2/18/2026, these objections have been withdrawn.
35 USC112(b) Rejections
Claims 8-9 and 12 were rejected due to various indefiniteness issues. In light of Applicant’s amendments to the claims submitted 2/18/2026, these rejections have been withdrawn.
35 USC 112(d) Rejections
Claim 12 was rejected for failing to include all of the limitations of the claim upon which it depends. In light of Applicant’s amendments to the claims submitted 2/18/2026, this rejection has been withdrawn.
35 USC 103 Rejections
Claims 1-20 were rejected under 35 U.S.C. 103 as being unpatentable over Fan (WO 2020/061529 A1) and various combinations of references.
Regarding the 35 USC 103 Rejections presented in the Non-Final Rejection mailed 11/20/2025, Applicant argues that Fan, the primary reference used in the rejections, does not meet the newly amended portion of claim 1, particularly where the barcodes in the sequence reads are flanked on both sides by portions of the target polynucleotide. Applicant argues in particular that Figure 3 of Fan and the teachings throughout the reference only teach read fragments where the barcodes are at the ends of the reads (Remarks, pages 13-15).
In the Non-Final Rejection, Figure 3 is recited as a main teaching in the rejection of claim 1, where the barcodes do appear at the end of the fragments. Similar teachings are shown in Figure 2. General alignment of read pairs is used in the working examples (e.g. paras. 74, 76, and 79), and paired end sequencing is also generally recited by the reference (see Figure 1a, for example). Thus, the Examiner agrees that Applicant’s amendments overcome the previous rejections.
Thus, the previous rejections are withdrawn, and see new grounds of rejection below.
Drawings
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they do not include the following reference signs mentioned in the description: reference characters 617 and 619, which should appear in Figure 6. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Interpretation
Regarding claim 1, the term “includes” is considered open language, where additional components may be used. Thus, the phrase “wherein a first read of the plurality of reads includes the first polynucleotide barcode,” does not preclude additional elements, such as the second polynucleotide barcode, from being in the first reads. See MPEP 2111.03.
It is noted that in claim 1, only the first and second reads need to include the first and first and second barcodes, respectively, flanked by portions of the target polynucleotide. The other reads of the plurality of reads may include the first and/or second barcodes anywhere in the read, including at the ends of the reads.
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, 5-6, 8-12, and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Fan (WO 2020/061529 A1, IDS ref), in view of Invitrogen (“DNA fragmentation strategies for next-generation sequencing library preparation,” 2019), and in view of Steemers et al. (WO 2012/061832 A1; cited in Applicant’s IDS).
Fan teaches compositions and methods for generating indexed nucleic acid samples via the use of transposons and fragmentation (Abstract). Generally, the reference teaches that a sample may be contacted with up to 1,000 transposon sequences, fragmented, sequenced, and analyzed (para. 3). Para. 43 describes exemplary transposons, where two barcode sequences may be used. Para. 64 shows an exemplary use of 5 different transposon inserts, each containing a barcode pair. After fragmentation and sequencing, read pairs are matched to identify the original nucleic acid sample. Some of the reads have only a single barcode, while some have two, as shown in Figure 3. By overlapping the barcode regions (see the dotted lines in Figure 3), the original sequence may be pieced together. Though Fan does not explicitly state that the first and second barcode sequences are removed to recreate the original nucleic acid sequence, this would be prima facie obvious, as the original sequence does not contain the transposon/barcode sequences. Throughout the reference, Fan states that the original sequences are discerned or reassembled (see e.g. paras. 37, 58, 62, 74), which would therefore indicate that the transposon/barcode sequences are not included in this final reassembly.
However, in Figure 3, and para. 64, which describes this figure, paired end sequencing methods appear to be used. Thus, the barcode sequences of Fan in this embodiment would be at the ends of each fragment.
In considering the general teachings of Fan, para. 16 notes sequencing via aligning adjacent fragments using transposons, where the transposons are not required to be at the ends of said fragments. The method of Fan is also generally described as an alternative to typical sequencing methods where nucleic acids are fragmented and then barcodes are appended at the end of each fragment, where instead barcode information is inserted into the original nucleic acid sequence before any such fragmentation (paras. 37-38). Para. 3 notes that in some embodiments, assembling the nucleic acid fragments further comprises analysis of paired end read data, implying that this is not required of every embodiment. In order to generate fragments, para. 50 of Fan notes that fragmentation can be done via targeted amplification with primers that target the transposon sequences, and this fragmentation would likely result in fragments such as those shown in Figure 3. However, additional fragmentation methods, such as endonuclease fragmentation or physical shearing, may be used.
Invitrogen teaches DNA fragmentation methods in the context of sequencing, and particularly focuses on physical and enzymatic shearing methods. The reference teaches that physical shearing breaks the covalent bonds the connect DNA in a random fashion (page 1, column 2, paras. 2-3 and page 2, para. 3). Enzymatic shearing utilizes endonucleases with relatively little bias (page 2, column 2, paras. 2 and 4 and Figure 2). The reference goes on to discuss the benefits of these methods, including the superior coverage of physical shearing with a consistent insert size and little sample-to-sample variation (page 1, “Summary” and page 2, column 1, para. 3), and that enzymatic shearing is highly scalable and may require less nucleic acid input (Summary).
As both of these fragmentation methods are taught by Fan, it would be prima facie obvious to use either of them in the methods of Fan described above. This would result in fragmentation of sequences where the barcodes are not present on the very ends of sequence reads, at least not for every sequence read. In para. 50 of Fan, primer design for fragmentation via amplification is described, and if this amplification was no longer needed, then there would be no need for this additional design and amplification step, simplifying the overall method. Invitrogen teaches that enzymatic and physical shearing methods have various advantages that would make them attractive means by which to fragment sequences. As these are all DNA fragmentation methods, the use of one over another would amount to simple substitution. 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.” Swapping PCR fragmentation for enzymatic or physical shearing fragmentation would still result in fragmented DNA, and so the results of this substitution would be predictable. Furthermore, there would be a reasonable expectation of success as Fan specifically notes that these fragmentation methods are compatible with their invention.
However, if enzymatic or physical shearing were employed in the method of Fan, then paired end sequencing could no longer be performed, as every sequence read would not be capped with the transposons. Fan provides additional teachings regarding the compatible of sequencing in their methods generally with enzymatic shearing (see para. 15), and notes that sequencing can still occur even if fragments only have a portion of a transposon nucleic acid (para. 16). Paras. 51-57 describe various sequencing methods that are compatible with the methods of Fan, and while paired-end sequencing is described, sequencing methods are not solely limited to paired-end methods. The reference does not provide many details on such alternative sequencing methods, however.
Steemers is drawn to the use of transposons as tags to analyze target nucleic acid sequences (Abstract). Page 46, paras. 2-3 describe a linked read strategy for analyzing and sequencing template nucleic acids. This method can link sequence reads based on the markers contained in those reads, where at least two markers (which can each contain barcodes) are linked, and are then used to link the surrounding target nucleic acid sequences to one another. (see also page 46, para. 4, and page 47, para. 3). Examples of linked read strategies are shown in Figures 28-31. Though several of these figures show that the barcodes may be at the end of fragments (e.g. Figure 28), this need not be the case in every instant (e.g. Figure 31).
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 guidance provided by Steemers to successfully sequence, align, and analyze the fragments of Fan in view of Invitrogen to arrive at the method of claim 1 above. Steemers points out that linked barcode sequences can be linked regardless of where they are within fragments, and thus can be used to align and sequence large nucleic acid fragments. As Fan already alludes to such sequencing, the linked read teachings of Steemers provide additional details on how such sequencing would operate within the context of the shearing fragmentation methods of Fan in view of Invitrogen described above, and provides a reasonable expectation of success that such shearing is in fact compatible with sequencing/sequencing analysis methods. As these reads are still used to generate the sequence of a larger target polynucleotide sequence, the general overlapping of the barcode regions and removal of these barcode sequences in the finally generated consensus sequence as stated above in para. 19 would still apply.
Thus, claim 1 is prima facie obvious over Fan, in view of Invitrogen, and in view of Steemers.
Regarding claim 5, Fan teaches that their methods can identify variants in a sample (paras. 52 and 65-66). In Figures 4A-4B, said variant is between the two barcode sequences on the sequence reads. Paras. 17 and 75-76 also discusses sequencing mutations. Taken together, the ordinary artisan would recognize that, as an indel is a type of mutation, it could be analyzed in the methods described by Fan, in view of Invitrogen, and in view of Steemers in the manner recited for other mutations – i.e. the mutation could be aligned when it is between the first and second barcodes.
Thus, claim 5 is prima facie obvious over Fan, in view of Invitrogen, and in view of Steemers.
Regarding claim 6, Fan teaches that the nucleic acid sample can comprise DNA (para. 39).
Regarding claims 8-9, Fan, in view of Invitrogen, and in view of Steemers teaches fragmentation via enzymatic or physical shearing, as described above. Para. 50 of Fan states that fragments can be enriched prior to sequencing with PCR.
Regarding claims 10-11, Fan teaches that the transposon sequences may include forward and reverse primer sites, as well as mosaic sequences that facilitate their insertion into a nucleic acid sample (para. 41). Thus, the transposon is acting as the probe sequence described by the instant claims. Specifically regarding claim 11, paras. 41 and 44 recite the use of “one or more” barcode sequences in a transposon, and para. 48 cites the use of “at least one barcode.” Para. 44 also states that up to 30,000 unique pairs of barcodes can be present in a transposon library used to conduct the methods of Fan. As Fan specifically teaches that a large number of pairs of barcodes may be used, and the sequencing of the combination of references is based on linked pairs of barcode, it would be prima facie obvious that barcode pairs additional to that described in the above teachings of Fan, in view of Invitrogen, and in view of Steemers, such as a third/fourth barcode pair, could be present in the transposon sequences.
Thus, claims 10-11 are prima facie obvious over Fan, in view of Invitrogen, and in view of Steemers.
Regarding claim 12, Fan teaches the use of more than two barcodes, as shown in Figure 3, and the use of additional barcode pairs in Fan, in view of Invitrogen, and in view of Steemers is prima facie obvious, as described above in the rejection of claims 10-11 . Para. 64 of Fan, which describes Figure 3, states that any number of different transposons can be used to assemble read pairs. The reference also teaches that multiple types of sequencing data can be combined to assemble the target sequences (para. 55). In their examples, Fan teaches that in order to effectively use the described methods, a sufficient number of read pairs must be generated (paras. 78 and 80). Figures 4A and 4B also show contrasting scenarios where in 4A, an insufficient number of read pairs is provided to map the target sequence, whereas in Figure 4B, a sufficient number of read pairs is provided. This is primarily because in Figure 4A, there is not sufficient barcode diversity for the region of interest that the variant sequence (403) cannot be mapped to region 402A or 402B.
Using these teachings, it would thus be prima facie obvious to the ordinary artisan that a method as described in claim 12 could be performed when utilizing the methods of Fan, in view of Invitrogen, and in view of Steemers in a manner that results in a scenario as shown in Figure 4A. Specifically, if the transposons and barcodes initially inserted into the sequences do not provide enough data to reliably reconstruct the target sequence, as is shown in Figure 4A, then additional transposons/barcodes would be needed. Thus, additional barcodes could be inserted into the targets to produce a scenario as shown in Figure 4B, and then the assembly of the target sequence would be based on the data generated from all of the transposon/barcode sequences. This would essentially involve repeating the method of Fan, in view of Invitrogen, and in view of Steemers as described above in the rejection of claim 1 to insert additional sequences, and as Fan teaches examples analyzing sequence reads with more than two barcodes, there would be a reasonable expectation of success.
Thus, claim 12 is prima facie obvious over Fan, in view of Invitrogen, and in view of Steemers.
Regarding claim 14, Fan teaches utilizing tag sequences, as well as the sequences adjacent to those tags, when determining sequence information. Specifically, this can include using tags and adjacent sequences to map reads to common sequences (paras. 32-33). Fan also generally teaches the alignment of adjacent fragments that contain at least a portion of the transposons in order to determine the sequence of a target (paras. 16 and 35). Though Fan does not state that tags and barcodes are interchangeable in their invention, the tags of Fan at least partially perform the same function as the barcodes of Fan in that they can be used to align sequence reads and aid in determining the original target sequence. Therefore, it would be prima facie obvious that the barcodes of Fan, in view of Invitrogen, and in view of Steemers described above in the rejection of claim 1 could be used in a manner similar to the tags described by Fan, and therefore could be used with adjacent sequences on the sequence reads to find common sequences and assemble the original sequence. This very thing is also alluded to by the linked read methods of Steemers described above, as this strategy takes sequences adjacent to the barcodes into account (page 46, paras. 3-4). This would also generally be obvious for the ordinary artisan to do when assembling the sequence reads, as each transposon will likely not insert into the target nucleic acids in the same exact spot, and so the same barcode may appear in slightly different spots throughout the target sequences in the sample. The ordinary artisan would therefore need to use sequences adjacent to the barcodes to fully align the fragmented sequence reads and determine the original target sequence. There would be a reasonable expectation of success in using these adjacent sequences because the entirety of the fragments are already sequenced in the method of Fan, in view of Invitrogen, and in view of Steemers, and so the sequencing data would already be available for use.
Thus, claim 14 is prima facie obvious over Fan, in view of Invitrogen, and in view of Steemers.
Claims 2-4, 7, 13, and 15-20 are rejected under 35 U.S.C. 103 as being unpatentable over Fan (WO 2020/061529 A1), in view of Invitrogen (“DNA fragmentation strategies for next-generation sequencing library preparation,” 2019), in view of Steemers et al. (WO 2012/061832 A1; cited in Applicant’s IDS), and further in view of Drmanac et al. (WO 2014/145820 A2).
Regarding claims 2-4, Fan, in view of Invitrogen, and in view of Steemers teaches the methods of claims 1, 5-6, 8-12, and 14, as described above. Fan also notes that their methods may reduce issues related to repetitive sequences (such as trinucleotide repeats; para. 31), but does not specifically teach embodiments in which repeat sequences are examined. Fan also teaches that the insertion points of the transposons do not have to be random, and can be influenced by reactions conditions/components (para. 48). Steemers states that targets in their methods may be repeats (page 34, para. 2), but does not provide any particular examples utilizing such targets.
Drmanac teaches methods and compositions for tagging long fragments of a target nucleic acid for analyzing sequencing information (Abstract). This is done via multiple tagging methods (para. 14). This combines targets with tags, fragments the targets, and then sequencing the fragments, where said fragments may contain one or more tags (para. 15). The reference teaches that this method can be used to analyze short tandem repeats (STRs), which include trinucleotide repeats (paras. 254-256). Drmanac teaches that STRs are important to analyze for forensic purposes (para. 254), and generally teaches that their methods can create consensus sequences even if long repeats in a sequence are present (para. 92).
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 provided by Drmanac to examine STRs, and specifically trinucleotide repeats, in the method of Fan, in view of Invitrogen, and in view of Steemers. Fan and Steemers already hint at examining such sequences in their methods, and Drmanac, which teaches a very similar method, explicitly notes that such sequences can be analyzed via the use of insertion sequences and tags/barcodes. Additionally, it is taught that examining repeats can come with challenges that are mitigated by the methods of Fan, in view of Invitrogen, and in view of Steemers, and that analyzing these sequences has practical use, which would motivate the ordinary artisan. Fan also teaches that the location of transposon insertion can be influenced, and thus the ordinary artisan can steer transposon insertion towards STRs/trinucleotide repeats. Also, in the case of long repeats on target nucleic acid fragments, it is likely that at least one of the barcode sequences of the transposon would be between repeat sequences. As Fan teaches that specific regions of interest in genomic DNA can be chosen as targets (para. 39), STR regions can even be targeted by the methods of the invention, furthering this likelihood. Therefore, a scenario such as that presented in instant claim 2 would occur simply through the targeting of the STR/trinucleotide sequences generally.
Thus, claims 2-4 are prima facie obvious over Fan, in view of Invitrogen, in view of Steemers, and further in view of Drmanac.
Regarding claim 7, Fan teaches that the target nucleic acids can be RNA, such as mRNA transcripts from a population of cells, or “other” RNA sources, but is not specific about what those sources may be, and does not specifically state using a sample that has different isoforms of RNA. The reference also teaches that their methods can identify SNPs (paras. 52 and 77-78). Steemers generally mentions that different isoforms can be reassembled with their specific methods (page 15, para. 1), but does not provide any further details.
Drmanac teaches analysis of mutations in splicing sites in transcribed RNA, and notes that these splicing differences may lead to disease (paras. 312-314). The reference also teaches that SNPs can create splice site variations (para. 317).
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 that in combining the teachings of Fan, in view of Invitrogen, and in view of Steemers and Drmanac, RNA could be examined from a sample that contains multiple isoforms (e.g. a sample containing sequences with alternative splicing sites). Fan already teaches the use of mRNAs as targets, as well as the examination of sequences with SNPs, and Steemers generally describes analyzing isoforms. Drmanac teaches that SNPs can generate alternative splicing sites, and provides reasoning for wanting to examine such sites (e.g. the examination of sites related to disease). In combining these teachings, the ordinary artisan would be motivated to examine alternative splice site SNPs in Fan, in view of Invitrogen, and in view of Steemers, and would thus require an RNA sample that contains a mutated and non-mutated sequence, so as to determine the specific sequence and location of said SNP for a given sample. There would be a reasonable expectation of success because such a sample can exist within a single patient suspected of having a particular disease, and so would not require any unusual sampling or sample preparation/combining methods.
Thus, claim 7 is prima facie obvious over Fan, in view of Invitrogen, in view of Steemers, and further in view of Drmanac.
Regarding claim 13, Fan teaches the use of nucleic acid samples from any natural or artificial source, including disease-related sources (para. 39). However, neither Fan nor Steemers teach sequencing the target nucleic acids before the insertion of the transposons.
Drmanac teaches mapping sequence reads to a reference genome (paras. 138, 199, 224, 250, 280, 291).
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 arrive at the invention of claim 13 via the teachings of both Fan, in view of Invitrogen, and in view of Steemers and Drmanac. Specifically, Fan teaches the use of any nucleic acids with their methods, and Drmanac teaches comparing the sequence assembled via use of their method with a reference sequence. If using a nucleic acid sample that contains unknown nucleic acid sequences, or sequences for which no reference samples exist, then one would be unable to compare the assembled target sequence with a reference sequence. Thus, in order to make comparisons with the assembled target sequence, the sample would have to be sequenced before the insertion of the transposon sequences. This would be useful as it would provide a means for determining the accuracy of the method/sequencing alignment for the assembled sequence. This would also allow for the determination of variant or mutant sequences present in a sample, as if there were discrepancies between the originally sequenced nucleic acid and the assembled nucleic acid sequence, it could indicate the presence of particular SNPs or other variants that may be associated with diseases such as cancer. As Fan teaches the use of disease-related samples, such an additional comparison would be effective in providing additional downstream data that may aid in patient diagnoses and outcomes. As both Fan and Drmanac teach various sequencing methods (e.g. Fan para. 53 and Drmanac para. 197) and these are well-known in the art, there would be a reasonable expectation of success.
Thus, claim 13 is prima facie obvious over Fan, in view of Invitrogen, in view of Steemers, and further in view of Drmanac.
Regarding claim 15, it is first noted that the operations described by the claim equate to the same limitations described by the method of claim 1. Fan, in view of Invitrogen, and in view of Steemers therefore reads on these limitations for the same reasons as described in the rejection of claim 1 above. Fan also teaches that computer-implemented systems can be used to assemble sequencing data, where said computer can comprise a processor that is configured to execute the methods of the invention (paras. 4 and 56), but does not specifically teach that a non-transitory computer readable medium can be used as recited in the claim. Steemers also does not recite such a medium.
Drmanac teaches that the methods of their invention can be carried out by a non-transitory computer readable storage medium that stores instructions, where the methods are carried out upon the execution of said instructions (paras. 330 and 339-341).
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 a non-transitory computer readable medium, such as the one described by Drmanac, in the invention of Fan, in view of Invitrogen, and in view of Steemers. Drmanac teaches that such a computer-readable storage medium can be used to execute the methods of their invention, which as described above in the rejection of claims 2-4, are very similar to those of Fan. Thus, the ordinary artisan would recognize that such a computer-readable storage medium could be used with the methods of Fan, in view of Invitrogen, and in view of Steemers, and this is further bolstered by Fan’s general teachings regarding use of computers that can execute their described methods, which would provide a reasonable expectation of success. The ordinary artisan would recognize that by implementing a computer system to automatically execute portions of the method, this would increase speed and efficiency in completing the method, and would allow for operators of the method to focus on aspects that cannot be done via computer. Therefore, using a computer-readable storage medium could allow for increased samples or replicates to be processed over time, which would increase the productivity and yield of results associated with the method.
Thus, claim 15 is prima facie obvious over Fan, in view of Invitrogen, in view of Steemers, and further in view of Drmanac.
Regarding claim 16, this claim recites the same limitations as instant claim 2 within the context of the computer-readable medium. As claim 2 was already rejected as obvious over Fan, in view of Invitrogen, in view of Steemers, and further in view of Drmanac as described above, claim 16 would also be rejected as obvious for the same reasons, along with the reasons described above in the rejection of claim 15.
Regarding claim 17, this claim recites the same limitations as instant claim 13 within the context of the computer-readable medium. As claim 13 was already rejected as obvious over Fan, in view of Invitrogen, in view of Steemers, and further in view of Drmanac as described above, claim 17 would also be rejected as obvious for the same reasons, along with the reasons described above in the rejection of claim 15.
Regarding claim 18, this claim recites the same limitations as instant claim 14 within the context of the computer-readable medium. As claim 14 was already rejected as obvious over Fan, in view of Invitrogen, and in view of Steemers as described above, claim 18 would also be rejected as obvious for the same reasons, along with the reasons described above in the rejection of claim 15 over Fan, in view of Invitrogen, in view of Steemers, and further in view of Drmanac.
Regarding claim 19, this expands on the limitations of claim 15 by requiring that a controller with a processor be used, where the processor executes the instructions of the non-transitory computer readable medium. It is noted that Applicant has not provided any specific definition for the term “controller.” As noted above, Fan teaches the use of processors that can receive sequence information and produce output (paras. 4-5), as well as execute the methods described by Fan (para. 56). Steemers does not recite controllers or processors.
Drmanac teaches the use of controllers connected to a computing device, where processors communicate with the connected components and execute system instructions (paras. 277-278).
Thus, both Fan and Drmanac teach that processors may be used to execute specific instructions of their methods, and Drmanac specifically teaches that these processors can be connected to controllers and operate within the computer systems described by the reference. The ordinary artisan would therefore recognize that the controller and processor could be added to the non-transitory computer-readable medium system of Fan, in view of Invitrogen, in view of Steemers, and further in view of Drmanac described above in the rejection of claim 15. MPEP 2143 I (A) states, “The rationale to support a conclusion that the claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination yielded nothing more than predictable results to one of ordinary skill in the art.” The processor and controller would still act as described by Drmanac, and as these pieces have already been shown to be able to execute computer instructions in methods the same as or similar to those of Fan and Drmanac, adding these to the invention of Fan, in view of Invitrogen, in view of Steemers, and further in view of Drmanac would not result in a change to the method of this combination of references, but would simply be added to the mechanism that executes said method, making the results of the combination predictable.
Thus, claim 19 is prima facie obvious over Fan, in view of Invitrogen, in view of Steemers, and further in view of Drmanac.
Regarding claim 20, this claim recites the same limitations as instant claim 18 within the context of the system with a controller/processor. As claim 18 was already rejected as obvious over Fan, in view of Invitrogen, in view of Steemers, and further in view of Drmanac as described above, claim 20 would also be rejected as obvious for the same reasons, along with the reasons described above in the rejection of claim 19.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FRANCESCA F GIAMMONA whose telephone number is (571)270-0595. The examiner can normally be reached M-Th, 7-5pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gary Benzion can be reached at (571) 272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/F.F.G./Examiner, Art Unit 1681
/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681