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 .
The Response of 18 Dec. 2025 has been entered.
Claims 1, 3, 5-7, 9, 11-15, 17-19, 21-27 and 29-33 are currently pending.
Claim 5 is withdrawn as being drawn to a nonelected species.
Claims 1, 3, 6, 7, 9, 11-15, 17-19, 21-27 and 29-33 are considered here with respect to the elected species of: of RT-LAMP as the amplification type, expected/determined fraction of positive samples as the basis for optimization, and an infectious agent as the target sequence.
Any rejection not reiterated herein has been withdrawn.
Response to Arguments
Applicant's arguments filed 18 Dec. 2025 have been fully considered but they are not persuasive.
Applicant argues that the claimed kit is distinguishable from the cited art in that it uses a compressed barcode space wherein individual barcodes from the defined set are present in multiple different primer sets in the kit. This is not persuasive because Anderson teaches a dual barcoding approach using n number of first barcodes and m number of second barcodes to give rise to n x m different barcode combinations. An n x m number of combinations would inherently require that individual barcodes are used in more than one set (see rejection, below)
Claim Objections
Claims 26 and 27 are objected to because of the following informalities:
Claims 26 and 27 should be amended as follows: "heating reaction components".
Appropriate correction is required.
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.
Claims 1, 3, 6, 7, 9, 11-15, 17-19, 21-27 and 29-33 are rejected under 35 U.S.C. 112(b) 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 1 recites “to generate amplicons that comprise the one or more target sequences and the unique combination of barcodes”. It is unclear whether the “unique combination” limitation applies to the set of amplicons that can be generated or to each amplicon individually. For purposes of applying prior art, the claim is construed as allowing either construction.
Claim 7 recites that "the barcodes are selected to avoid barcodes having a sequence portion that is the reverse complement to the 3' end of a forward inner primer (FIP) or a backward inner primer (BIP)". The recited selection is a product-by-process limitation that is limiting only with respect to any structure necessarily implied by the process (selection) (see MPEP 2113). It is unclear what structure is implied by the recited selection to avoid barcodes having a sequence portion that is the reverse complement to the 3' end of a FIP/BIP - e.g., it is unclear what extent of reverse complementarity would be allowable within the scope of the claims (2 bases, 3 bases, 4 bases, or some other number?).
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 15 is rejected under 35 U.S.C. 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 15 recites that "the amplification reagents are isothermal amplification reagents, polymerase chain reaction reagents, or both". Claim 15 depends from claim 1, which has been amended to recite that the amplification reagents are for LAMP or RT-LAMP. Thus, claim 15 is broader than amended claim 1.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 103
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.
Claims 1, 3, 6, 9, 11-15, 29, 32 and 33 are rejected under 35 U.S.C. 103 as being unpatentable over the combination of Liang et al., Advances and Clinical Practice in Pyrosequencing. New York, NY: Springer New York, 2016. 243-255 in view of WO2012162267 to Anderson et al. (each previously cited).
Regarding claims 1, 3, 29, 32 and 33, Liang teaches a method and associated materials for multiplex RT-LAMP detection of viral pathogens, including RNA viruses (e.g., HCV, HBV, etc.), wherein the method uses LAMP primers that comprise a barcode sequence and are configured to amplify target viral sequences from a blood sample and generate amplicons comprising the target sequences and a unique barcode sequence that allows for identification of target amplicons (p. 244, 2nd full ¶ to p. 246, last ¶; under 3. Methods; p. 251, 1st ¶ to p. 253, last ¶). The method included four RT-LAMP primer sets for detection of four distinct viruses (under 4.1. Specificity). The LAMP primer sets each included a FIP primer and a BIP primer, with a barcode sequence on the FIP primer (p. 244, last ¶; 3.1 Multiplex LAMP Reaction).
Regarding claim 3, Liang teaches barcodes between two target-specific sequences on the FIP (Fig. 1).
Regarding claims 12 and 13, Liang teaches use of 3-nucleotide barcodes (4.5 Pyrosequencing on Nicked Multiplex LAMP Products), but also teaches that barcodes of n bases can be designed to encode 2n different targets (p. 246, 1st full ¶). Liang further teaches that the pyrosequencing step is capable of accurately identifying 10-bp barcode sequences (p. 251, 1st ¶). It would have thus been obvious to use up to 10-bp barcode sequences in view of Liang, and one would have been motivated to use longer (e.g., 10 bp) sequences in order to selectively identify a larger number of target amplicons (e.g., 20).
Regarding claim 14, Liang teaches that the method is carried out with equal concentrations of the barcoded FIP primers (under 3.1 Multiplex LAMP Reaction).
Regarding claim 15, Liang further teaches LAMP reagents, including enzymes (reverse transcriptase, DNA polymerase), dNTPs, buffer, etc. (under 3.1 Multiplex LAMP Reaction).
Regarding claims 24-26, Liang teaches carrying out the amplification reaction at 65 °C (under 3.1 Multiplex LAMP Reaction).
Claims 1, 3, 6, 9, 11-15, 29, 32 and 33 differ from Liang in that: the claims are directed to a kit comprising the LAMP primers and amplification reagents (claim 1); each primer set comprises a unique combination of barcodes having at least two barcodes, and the primer sets are configured to amplify one or more target sequences from a sample in one or more amplification steps to generate amplicons that comprise the one or more target sequences and the unique combination of barcodes (claim 1); individual barcodes from the defined set are present in multiple different primer sets in the kit such that different primer sets comprise different unique combinations of barcodes (claim 1); and at least two of the primers of at least one of the one or more primer sets are barcoded (claim 11).
Anderson teaches a method for generating a barcoded amplicon via an isothermal amplification reaction using dual barcoded primers, thereby generating an amplicon with a combination of first and second barcode sequences (entire doc, including [0004]-[0023]). The dual barcoding allows for generating a plurality of combinatorially tagged target nucleotide sequences/amplicons, including N x M different first and second barcode combinations (where N is the number of first barcodes and M is the number of second barcodes) ([0007]-[0008]; [0135]-[0146]; [0316]-[0324], esp. [0318]). Anderson further teaches kits for carrying out sequencing/amplification methods using the primers, which can comprise primers, polymerases, reagents, a container/vessel and "other material(s) that may be desirable from a user standpoint, such as a buffer(s), a diluent(s), a standard(s), and/or any other material useful in sample processing, washing, or conducting any other step of the assay" ([0316]-[0324]).
It would have been obvious to one of ordinary skill in the art at the time the invention was made to assemble the primer sets of Liang and any other reagents/materials useful for carrying out a LAMP detection/amplification as taught by Liang in a kit as taught by Anderson because it would have been obvious to combine prior art elements according to known methods to yield predictable results. One of ordinary skill would have been motivated to assemble the primers of Liang and other materials for carrying out a LAMP amplification/detection in a kit as taught by Anderson because doing so would provide a simple means for carrying out the method at a site of interest. Assembling the primers of Liang and other materials for carrying out a LAMP amplification/detection in a kit as taught by Anderson would have led to predictable results with a reasonable expectation of success because Anderson teaches such kits for a substantially similar isothermal amplification reaction as in Liang. Moreover, making such a kit would require only assembling the various materials taught by Liang/Anderson in a single package/collection.
It would have further been obvious to one of ordinary skill in the art at the time the invention was made to use two barcode sequences for each primer set of Liang (such that each primer set comprises a unique combination of two barcodes and the resulting amplicons comprise said unique combination), as taught by Anderson, because it would have been obvious to combine prior art elements according to known methods to yield predictable results. One of ordinary skill would have been motivated to use a second barcode sequence in primer sets of Liang because Anderson teaches that dual barcoding allows for generating a plurality of combinatorially tagged target nucleotide sequences, including N x M different first and second barcode combinations (allowing for labeling of a large number of potential target amplicons). Using a second barcode sequence in the primer sets of Liang would have led to predictable results with a reasonable expectation of success because Anderson teaches that dual barcoding of primers can be used for isothermal amplifications such as the LAMP amplification of Liang.
Regarding the recitation in claim 1 that "the barcodes are selected from a defined set of barcode sequences", the recited selection is a product-by-process limitation that is limiting only with respect to any structure necessarily implied by the process (selection) (see MPEP 2113). Any given set of barcodes is selectable from some defined set of barcodes, and as such the recited selection does not distinguish the claims from the cited combination.
Regarding the recitation in claim 1 that "individual barcodes from the defined set are present in multiple different primer sets in the kit", Anderson teaches that the dual barcoding using n number of first barcodes and m number of second barcodes gives rise to n x m different barcode combinations. An n x m number of combinations would inherently require that individual barcodes are used in more than one set, and it would have been obvious to do so in order to maximize the number of unique combinations from given n and m numbers of barcode sequences.
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over the combination of Liang in view of Anderson, as applied to claims 1, 3, 6, 9, 11-15, 29, 32 and 33, further in view of US 20210355526 to Nissan et al., as evidenced by Schmid-Burgk et al., biorxiv (2020): 2020-04 (cited in IDS of 30 Sept. 2022).
Claim 7 differs from the combination of Liang in view of Anderson, as applied to claims 1, 3, 6, 9, 11-15, 29, 32 and 33, in that: the barcodes are selected to avoid barcodes having a sequence portion that is the reverse complement to the 3' end of a forward inner primer (FIP) or a backward inner primer (BIP).
Nissan teaches use of barcoded primers for labeling amplicons, and further teaches criteria for the selection of such primers that includes avoidance sequences leading to secondary structure formation and hybridization with other barcodes, including avoidance of reverse complementary sequences between any pair of barcodes ([0012]; [0047]-[0054]).
Schmid-Burgk evidences that the avoidance of barcodes having a sequence portion that is the reverse complement to the 3' end of a BIP or FIP as recited in claim 7 is to avoid formation of secondary structure that can interfere with amplification (p. 8, last ¶ to p. 9, 1st ¶; cf. published Spec. US20230151441, [0672]).
It would have been obvious to one of ordinary skill in the art at the time the invention was made to select FIP/BIP barcodes for use in the kit of Liang in view of Anderson so as to avoid secondary structure formation and/or barcode hybridization (including avoiding barcodes having a sequence portion that is the reverse complement to any FIP or BIP sequence) because it would have been obvious to combine prior art elements according to known methods to yield predictable results. One of ordinary skill would have been motivated to select barcodes in the method of Liang in view of Anderson so as to avoid secondary structure formation and/or barcode hybridization because Nissan teaches that such criteria provide for more accurate sequencing data from the amplification (see [0054]). Selecting barcodes in the method of Liang in view of Anderson so as to avoid secondary structure formation and/or barcode hybridization would have led to predictable results with a reasonable expectation of success because Nissan teaches such criteria in a similar amplification method (PCR) and predicting hybridization and/or secondary structure formation is well within the skill of the relevant art.
Claims 17-19 and 21-27 are rejected under 35 U.S.C. 103 as being unpatentable over the combination of Liang in view of Anderson, as applied to claims 1, 3, 6, 9, 11-15, 29, 32 and 33, further in view of US20200048722 to Nyan (previously cited).
Claims 17-19 and 21-27 differ from the combination of Liang in view of Anderson, as applied to claims 1, 3, 6, 9, 11-15, 29, 32 and 33, in that: the kit further comprises a lysis reagent (claim 17); the kit further comprises a control template DNA or RNA sequence (claim 18); the kit further comprises a sample collection component (claim 19); the kit further comprises a sample dosing component (claim 21); the kit further comprises a reaction vessel comprising a pre-mixed combination of amplification reagents and barcoded primers and configured to be sealed after receiving the sample, sample collection component, sample dosing component, or a combination thereof (claim 22); the reaction vessel is configured for use in an isothermal amplification reaction conducted at a point of care (claim 23); the kit further comprises one or more heating reaction components configured for use in an isothermal reaction conducted at a temperature between 45° C. to 75° C (claim 24), 55° C. to 70° C (claim 25), and 60° C. to 65° C (claim 26); and the heating components is or includes one or more chemical heating reagents (claim 27).
Nyan teaches methods and kits for performing a substantially similar multiplex RT-LAMP amplification reaction as in Liang for detection of viral target sequences, including several of the same viruses detected by Liang (HCV, HBV and HIV) (entire doc, including [0005]-[0010]; [0126]-[0164]). Nyan further teaches kits comprising materials/reagents useful for carrying out the amplification, including: primer sets, which can be provided in a container suitable for the amplification reaction (e.g., a tube, bottle, etc.; i.e. a reaction vessel); and reagents for carrying out the reaction/method ([0164]).
Regarding claim 17, Nyan teaches that the kit can comprise a lysis buffer (i.e. lysis reagent) suitable for lysing a pathogen in a blood sample ([0137]-[0138]; [0164]).
Regarding claim 18, Nyan teaches that the kit can comprise positive and/or negative control viral nucleic acids/templates ([0164]).
Regarding claim 19, Nyan teaches that the primers can be supplied in a container (e.g., bottle, tube, etc.) suitable for carrying out the amplification ([0164]) and any such container would be suitable for receiving a liquid sample (which would be necessary to carry out the reaction).
Regarding claim 21, the specification states that the dosing component can be fluid handling/sampling device, such as spoons, spatulas, depression sticks, droppers, capillaries, syringes, and the like (Spec., [0173]). Nyan teaches that sample can be obtained from “clinical biological samples including, but not limited to, cells, tissues, blood, serum, plasma, urine, cerebrospinal fluid, nasopharyngeal aspirates, middle ear fluids, bronchoalveolar lavage, tracheal aspirates, sputum, vomitus, buccal swabs, vaginal swabs, stool, and rectal swabs” ([0127]), and that a “further object of this invention is to provide a commercially practicable detection method that is portable, inexpensive, and field-deployable” ([0004]). It would have thus been obvious to include in the kit any sampling and/or fluid handling tools needed to carry out the method in the field (e.g., syringes or the like).
Regarding claim 22, Nyan teaches that the primers can be supplied in liquid form in a container (e.g., bottle, tube, etc.) suitable for carrying out the amplification ([0164]), and any such container would be sealable in order to maintain the liquid reagents and prevent contamination thereof.
Regarding claim 23, Nyan teaches that an “object of this invention is to provide a commercially practicable detection method that is portable, inexpensive, and field-deployable” and that the “assay is developed for laboratory as well as point-of-care and field epidemiological application” ([0004]; [0005]). It would have thus been obvious to use a reaction vessel suitable for such applications.
Regarding claims 24-26, Nyan teaches that the amplification can be carried out in a “one-step, closed-tube amplification procedure, using a single incubation temperature between 40 to 75° C. for about 10 to 40 minutes, on a real-time portable multichannel heat device” ([0130]). It would have thus been obvious to include such a portable heating device in the kit, in order to provide all materials needed to carry out the method (in line with the stated goal of allowing the amplification/detection to be carried out at point-of-care/in-field).
Regarding claim 27, a “chemical heating reagent” could include, e.g., any fossil fuel used to generate heat, either directly or indirectly (e.g., via generation of electricity in a generator), and it would have been obvious that any such reagents could be supplied in a kit for carrying out the detection/amplification.
It would have been obvious to one of ordinary skill in the art at the time the invention was made to make a kit for RT-LAMP detection of viral targets comprising dual barcoded primers as taught by the combination of Liang in view of Anderson because it would have been obvious to combine prior art elements according to known methods to yield predictable results. One of ordinary skill would have been motivated to assemble the primers of Liang in view of Anderson and other materials for carrying out a LAMP amplification/detection in a kit as taught by Nyan because doing so would provide a simple means for carrying out the method at a site of interest. Assembling the primers of Liang in view of Anderson and other materials for carrying out a LAMP amplification/detection in a kit as taught by Nyan would have led to predictable results with a reasonable expectation of success because Nyan teaches such kits for a substantially similar isothermal amplification reaction as in Liang in view of Anderson. Moreover, making such a kit would require only assembling the various materials taught by Liang/Anderson/Nyan in a single package/collection.
Claim 30 is rejected under 35 U.S.C. 103 as being unpatentable over the combination of Liang in view of Anderson and Nyan, as applied to claims 17-19 and 21-27, further in view of Hoffmann et al., Veterinary microbiology 139.1-2 (2009): 1-23 (previously cited).
Claim 30 differs from the combination of Liang in view of Anderson and Nyan, as applied to claims 17-19 and 21-27, in that: the kit further comprises control primers that are configured to amplify a target sequence of an endogenous RNA of the sample to confirm successful sample collection.
Hoffmann teaches that use of an internal positive control is important in nucleic acid amplification methods involving biological samples, to ensure adequate efficiency of RNA extraction and to avoid false negative results (under 1.2. Internal controls). The internal control can be a nucleic acid endogenous to the sample that is co-amplified with target nucleic acids, such as a housekeeping gene (e.g., beta-actin) (under 1.2. Internal controls).
It would have been obvious to one of ordinary skill in the art at the time the invention was made to make a kit for RT-LAMP detection of viral targets as taught by the combination of Liang in view of Anderson and Nyan wherein the kit includes primers for an endogenous internal positive control as taught by Hoffmann because it would have been obvious to combine prior art elements according to known methods to yield predictable results. One of ordinary skill would have been motivated to include primers for an endogenous internal positive control as taught by Hoffmann in the kit of Liang in view of Anderson and Nyan because Hoffmann teaches that such controls are important for ensuring adequate efficiency of RNA extraction and avoiding false negative results. Including primers for an endogenous internal positive control as taught by Hoffmann in the kit of Liang in view of Anderson and Nyan would have led to predictable results with a reasonable expectation of success because Nyan teaches that the kits can include materials for suitable positive and negative controls and that such controls can be selected by one skilled in the art (Nyan, [0164]), and Hoffmann teaches that such endogenous internal positive controls are commonly used in amplification methods using biological samples.
Claim 31 is rejected under 35 U.S.C. 103 as being unpatentable over the combination of Liang in view of Anderson and Nyan, as applied to claims 17-19 and 21-27, further in view of Ahn et al., BMC infectious diseases 19.1 (2019): 676 (previously cited).
Claim 31 differs from the combination of Liang in view of Anderson and Nyan, as applied to claims 17-19 and 21-27, in that: the kit further comprises a colorimetric or turbidimetric indicator.
Ahn teaches a method for multiplex RT-LAMP based detection of viruses in biological samples, wherein positive RT-LAMP reactions are detected visually with the colorimetric indicator phenol red upon decreased pH from DNA polymerase activity (p. 3, last ¶). The method also included confirmation of results via other means (gel electrophoresis) (p. 3, last ¶).
It would have been obvious to one of ordinary skill in the art at the time the invention was made to make a kit for RT-LAMP detection of viral targets as taught by the combination of Liang in view of Anderson and Nyan wherein the kit includes a colorimetric indicator as taught by Ahn because it would have been obvious to combine prior art elements according to known methods to yield predictable results. One of ordinary skill would have been motivated to include a colorimetric indicator as taught by Ahn in the kit of Liang in view of Anderson and Nyan in order to allow for an instantaneous preliminary indication of a positive result (e.g., which could be confirmed via additional pyrosequencing). Including a colorimetric indicator as taught by Ahn in the kit of Liang in view of Anderson and Nyan would have led to predictable results with a reasonable expectation of success because Ahn teaches use of such an indicator in a substantially similar method of multiplex RT-LAMP detection of viral targets in a biological sample as taught by Liang in view of Nyan.
Conclusion
No claim is allowed.
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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/ROBERT J YAMASAKI/Primary Examiner, Art Unit 1657