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 .
Claim Interpretation
Attention is directed to MPEP 904.01 [R-08.2012].
The breadth of the claims in the application should always be carefully noted; that is, the examiner should be fully aware of what the claims do not call for, as well as what they do require. During patent examination, the claims are given the broadest reasonable interpretation consistent with the specification. See In re Morris, 127 F.3d 1048, 44 USPQ2d 1023 (Fed. Cir. 1997). See MPEP § 2111 - § 2116.01 for case law pertinent to claim analysis.
It is noted with particularity that narrowing limitations found in the specification cannot be inferred in the claims where the elements not set forth in the claims are linchpin of patentability. In re Philips Industries v. State Stove & Mfg. Co, Inc., 186 USPQ 458 (CA6 1975). While the claims are to be interpreted in light of the specification, it does not follow that limitations from the specification may be read into the claims. On the contrary, claims must be interpreted as broadly as their terms reasonably allow. See Ex parte Oetiker, 23 USPQ2d 1641 (BPAI, 1992). In added support of this position, attention is directed to MPEP 2111 [R-11.2013], where, citing In re Prater, 415 F.2d 1393, 1404-05, 162 USPQ 541, 550-51 (CCPA 1969), is stated:
The court explained that “reading a claim in light of the specification, to thereby interpret limitations explicitly recited in the claim, is a quite different thing from ‘reading limitations of the specification into a claim,’ to thereby narrow the scope of the claim by implicitly adding disclosed limitations which have no express basis in the claim.” The court found that applicant was advocating the latter, i.e., the impermissible importation of subject matter from the specification into the claim.
Additionally, attention is directed to MPEP 2111.01 [R-01.2024], wherein is stated:
II. IT IS IMPROPER TO IMPORT CLAIM LIMITATIONS FROM THE SPECIFICATION
“Though understanding the claim language may be aided by explanations contained in the written description, it is important not to import into a claim limitations that are not part of the claim. For example, a particular embodiment appearing in the written description may not be read into a claim when the claim language is broader than the embodiment.” Superguide Corp. v. DirecTV Enterprises, Inc., 358 F.3d 870, 875, 69 USPQ2d 1865, 1868 (Fed. Cir. 2004).
Attention is also directed to MPEP 2111.02 II [R-07.2022]. As stated herein:
II. PREAMBLE STATEMENTS RECITING PURPOSE OR INTENDED USE
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The claim preamble must be read in the context of the entire claim. The determination of whether preamble recitations are structural limitations or mere statements of purpose or use "can be resolved only on review of the entirety of the [record] to gain an understanding of what the inventors actually invented and intended to encompass by the claim" as drafted without importing "'extraneous' limitations from the specification." Corning Glass Works, 868 F.2d at 1257, 9 USPQ2d at 1966. If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction. Shoes by Firebug LLC v. Stride Rite Children’s Grp., LLC, 962 F.3d 1362, 2020 USPQ2d 10701 (Fed. Cir. 2020) (The court found that the preamble in one patent’s claim is limiting but is not in a related patent); Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1305, 51 USPQ2d 1161, 1165 (Fed. Cir. 1999). See also Rowe v. Dror, 112 F.3d 473, 478, 42 USPQ2d 1550, 1553 (Fed. Cir. 1997) ("where a patentee defines a structurally complete invention in the claim body and uses the preamble only to state a purpose or intended use for the invention, the preamble is not a claim limitation")… (Emphasis added)
Attention is directed to MPEP 2111 [R-10.2019]. As stated therein:
During patent examination, the pending claims must be "given their broadest reasonable interpretation consistent with the specification." The Federal Circuit’s en banc decision in Phillips v. AWH Corp., 415 F.3d 1303, 1316, 75 USPQ2d 1321, 1329 (Fed. Cir. 2005) expressly recognized that the USPTO employs the "broadest reasonable interpretation" standard:
The Patent and Trademark Office ("PTO") determines the scope of claims in patent applications not solely on the basis of the claim language, but upon giving claims their broadest reasonable construction "in light of the specification as it would be interpreted by one of ordinary skill in the art." In re Am. Acad. of Sci. Tech. Ctr., 367 F.3d 1359, 1364[, 70 USPQ2d 1827, 1830] (Fed. Cir. 2004). Indeed, the rules of the PTO require that application claims must "conform to the invention as set forth in the remainder of the specification and the terms and phrases used in the claims must find clear support or antecedent basis in the description so that the meaning of the terms in the claims may be ascertainable by reference to the description." 37 CFR 1.75(d)(1). (Emphasis added).
Attention is directed to MPEP 2173.04 [R-10.2019]. As stated therein:
Breadth of a claim is not to be equated with indefiniteness. In re Miller, 441 F.2d 689, 169 USPQ 597 (CCPA 1971); In re Gardner, 427 F.2d 786, 788, 166 USPQ 138, 140 (CCPA 1970) ("Breadth is not indefiniteness."). A broad claim is not indefinite merely because it encompasses a wide scope of subject matter provided the scope is clearly defined. But a claim is indefinite when the boundaries of the protected subject matter are not clearly delineated and the scope is unclear. For example, a genus claim that covers multiple species is broad, but is not indefinite because of its breadth, which is otherwise clear. But a genus claim that could be interpreted in such a way that it is not clear which species are covered would be indefinite (e.g., because there is more than one reasonable interpretation of what species are included in the claim). (Emphasis added)
Claim Rejections - 35 USC § 112, first paragraph / (a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1 and 7 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
For convenience claims 1 and 7 are reproduced below.
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As evidenced above, the method of claim 1 requires “subjecting the reaction mixture to an amplification condition”. The method of claim 1 does not require that the “pair of oligonucleotide probes” be removed prior to performing the amplification reaction. Likewise, the claimed method does not require that “primers” be used. Given such, the “probes” have been interpreted as also allowing for their use as a primer in an amplification reaction. Dependent claim 7 specifies that “each probe is modified at the 3’ end to prevent polymerase reaction.” It stands to reason that if the probes cannot be used in the amplification reaction, and the claimed method does not recite any step whereby primers are introduced and the blocked hybridized probes are removed, one would not be able to perform the requisite amplification step.
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.
Admissions as Prior Art.
Attention is directed to MPEP 2129 Admissions as Prior Art [R-07.2022], which states in part:
I. ADMISSIONS BY APPLICANT CONSTITUTE PRIOR ART
A statement by an applicant in the specification or made during prosecution identifying the work of another as "prior art" is an admission which can be relied upon for both anticipation and obviousness determinations, regardless of whether the admitted prior art would otherwise qualify as prior art under the statutory categories of 35 U.S.C. 102. Riverwood Int’l Corp. v. R.A. Jones & Co., 324 F.3d 1346, 1354, 66 USPQ2d 1331, 1337 (Fed. Cir. 2003); Constant v. Advanced Micro-Devices Inc., 848 F.2d 1560, 1570, 7 USPQ2d 1057, 1063 (Fed. Cir. 1988). Where the admitted prior art anticipates the claim but does not qualify as prior art under any of the paragraphs of 35 U.S.C. 102, the claim may be rejected as being anticipated by the admitted prior art without citing to 35 U.S.C. 102.
Attention is also directed to Ex parte Shirley, (BPAI, 2009) Appeal No. 2009002352, which, at pages 21 and 26, states:
The Specification’s omission of the term “prior art” and inclusion of the prior-art disclaimer may initially appear to indicate that Appellants do not consider the single-step soft bake process to constitute prior art. To place these latter, contraindicative factors into the proper context though, we note that patent-application drafters regularly endeavor to avoid the indiscriminate or imprudent use of the descriptive label, “prior art.” See Riverwood Intern. Corp. v. R.A. Jones & Co., Inc., 324 F.3d 1346, 1354 (Fed. Cir. 2003) (citing In re Fout, 675 F.2d 297, 300 (CCPA 1982)) for the proposition that “section 102 is not the only source of … prior art. Valid prior art may be created by the admissions of the parties”); In re Nomiya, 509 F.2d 566, 571 (CCPA 1975) (holding that an Applicant’s labeling of certain figures as “prior art,” ipsissimis verbis, constituted an admission that the pictured subject matter was prior art relative to Applicant’s invention); MPEP § 21294 (instructing that “the examiner must determine whether the subject matter identified as ‘prior art’ is applicant’s own work, or the work of another. In the absence of another credible explanation, examiners should treat such subject matter as the work of another”).
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The Specification’s omission of the term “prior art” and inclusion of the boilerplate prior-art disclaimer do not change our conclusion. In view of the record as a whole, these factors are ineffective in shielding Appellants from having their prior-art admissions treated as such.
Holding and Rationale
Claims 1-10 are rejected under 35 U.S.C. 103 as being unpatentable over US 2008/0038743 A1 (Gocke) in view of US 2004/0191821 A1 (Yanagihara et al.), US 2005/0069936 A1 (Diamond et al.), US 2015/0089681 A1 (Van Der Oust et al.), US 5,641,628 (Bianchi), US 2013/0115601 (Bunce et al.),US 7,256,035 B1 (Schnell et al.), US 2014/0287410 A1 (Shafer) and US 2012/0178648 A1 (Kawase et al.).
Gocke, in paragraph [0084] teach of a method for enriching a target mutant nucleic acid. As disclosed therein:
[0084] Enrichment of the target or mutated nucleic acid, whereby the concentration of the target nucleic acid is increased with respect to wild-type or non-mutated nucleic acid, may be accomplished by using an endonuclease either before or during an amplification step… (Emphasis added)
Yanagihara et al., in claim 33, claim primes that can be used in the amplification of nucleic acids that are suspected of comprising a mutation. As set forth therein:
33. A kit for determining if a double stranded nucleic acid target of interest contains a mismatch, comprising a) a Mu-end nucleic acid, b) a phage Mu transposase, and c) means for determining if the Mu-end nucleic acid transposes into the target at a predominant site and/or d) instructions for determining if the double stranded nucleic acid target contains a mismatch, and, optionally, further comprising, e) oligonucleotide primers suitable for amplification of a nucleic acid fragment comprising a portion suspected of containing a mutation, and/or f) means for labeling the Mu-end nucleic acid, and/or g) a preformed gel. (Emphasis added)
Diamond et al., at paragraph [0173], teach:
[0173] Analysis of point mutations in DNA can also be carried out by using the polymerase chain reaction (PCR) and variations thereof. Mismatches can be detected by competitive oligonucleotide priming under hybridization conditions where binding of the perfectly matched primer is favored (Gibbs et al., Nucl. Acids. Res. 17:2437-2448 (1989)). In the amplification refractory mutation system technique (ARMS), primers are designed to have perfect matches or mismatches with target sequences either internal or at the 3' residue (Newton et al., Nucl. Acids. Res. 17:2503-2516 (1989)).
The aspect of the primers comprising a mismatch that is internal is deemed to fairly suggest limitations of claim 6.
Applicant, at paragraph [0033] teaches:
[0033] In some embodiments of any one of the provided methods, the DSN enzyme is a DNA guided or RNA guided enzyme. In some embodiments of any one of the provided methods, the enzyme is an RNA guided enzyme, e.g., Cas9. In some embodiments of any one of the provided methods, the enzyme is a DNA guided enzyme, e.g., an Argonaute enzyme. (Emphasis added)
Van Der Oost et al., at paragraph [0052], teach using the DSN nuclease Argonaute.
In some instances, an Argonaute protein binds a DNA and cleaves the DNA. In some instances, the Argonaute protein binds a double-stranded DNA and cleaves a double-stranded DNA. (Emphasis added)
Bianchi, at column 8, lines 17-19, teach:
If amplification is to be carried out, the sorted samples are amplified for an appropriate number of cycles of denaturation and annealing (e.g., approximately 24-60).
The above presentation is deemed to fairly suggest limitations of claims 1-3 and 10.
Bunce et al., at paragraph [0133], teach the benefits of using an organic solvent when amplifying a nucleic acid. As disclosed therein:
To overcome the problems associated with the amplification of GC-rich genes (and/or using GC-rich primers), several approaches have been developed. Organic molecules such as dimethyl sulfoxide (DMSO), glycerol, polyethylene glycol, formamide, betaine, 7-deaza-dGTP, and dUTP have been included in the reaction mixture and have been shown to improve the amplification of GC-richDNA sequences (Baskaran et al., 1996; Chakrabarti and Schutt, 2001; Henke et al., 1997; Kang et al., 2005; Musso et al., 2006; Mutter and Boynton, 1995; Pomp and Medrano, 1991; Sidhu et al 11996; Sun et al., 1993; Turner and Jenkins, 1995; Weissensteiner and Lanchbury, 1996). (Emphasis added)
The above showing is deemed to fairly suggest limitations of claim 4.
Schnell et al., at column 3, first full paragraph, teach:
Thus, for purposes of nucleic acid amplification, such a device should be capable of cycling the temperature of the amplification reaction mixture between a denaturing temperature T.sub.1 (which can be in the range of about 80-105.degree. C. and preferably 90-100.degree. C.) and an annealing/extension temperature T.sub.2 (which can be in the range of about 30-90.degree. C. and preferably 50-70.degree. C.) where T.sub.1>T.sub.2 as is known to those skilled in the art. (Emphasis added)
The above showing is deemed to fairly suggest limitations of claim 5.
Shafer, at paragraph [0143], teach of using probes “having a 3' end modified to inhibit or prevent 3' polymerase extension”. (Emphasis added)
The above presentation is deemed to fairly suggest limitations of claim 7.
Kawase et al., at paragraph [0072], teach of detecting multiple target nucleic acid sequences. As disclosed therein:
When the present method is to detect multiple target nucleic acids 10 having multiple target sequences 12 constituting mutations, the second primer 40 may have the common partial sequence 44 which allows amplification of multiple target nucleic acids 10 having multiple target sequences 12 constituting mutations under the same condition.
The above presentation is deemed to fairly suggest limitations of claim 9.
In view of the above presentations, it would have been quite obvious at the time of the invention to have modified the method of Gocke whereby the enrichment of mutations comprised the amplification of such mutated sequences with primers that had the mutation internal, and to have removed the wild type/normal sequences through the use of a DSN such as Argonaute which would cleave the double-stranded nucleic acids, therein enriching the target nucleic acid that comprises the mutation.
In view of the detailed guidance, said ordinary artisan would have been both motivated and would have had a most reasonable expectation of success.
In view of the above presentation and in the absence of convincing evidence to the contrary, claims 1-10 are rejected under 35 U.S.C. 103 as being unpatentable over US 2008/0038743 A1 (Gocke) in view of US 2004/0191821 A1 (Yanagihara et al.), US 2005/0069936 A1 (Diamond et al.), US 2015/0089681 A1 (Van Der Oust et al.), US 5,641,628 (Bianchi), US 2013/0115601 (Bunce et al.), and US 2012/0178648 A1 (Kawase et al.).
Claims 11-22 are rejected under 35 U.S.C. 103 as being unpatentable over US 2009/0148842 A1 (Gormley et al.) in view of US 2012/0027870 A1 (Louwagie), US 2014/0193819 A1 (Hellyer et al.), US 2010/0203532 A1 (Makrigiorgos), US 2015/0089681 A1 (Van Der Oust et al.), US 7,396,678 B1 (Kolodner et al.), and US 2010/0068704 A1 (Christensen).
Gormley et al., at paragraph [0035], teach:
The fragmented double stranded nucleic acid target fragments are ligated to the forked adaptors and then split into two portions, one of which is treated with sodium bisulfite. Both portions are then amplified and sequenced to determine the differences between the treated and untreated portions. FIG. 2(a) depicts the steps of fragmenting a complex sample such as genomic DNA to generate a plurality of target duplex fragments, ligation of the target duplex fragments to mismatch (forked) adaptors to generate adaptor-template constructs and removal of unbound adaptors. (Emphasis added)
Gormley et al., has not been found to disclose employing preferential denaturation.
Louwagie, in paragraph [0060]
Bisulphite treatment may occur before or after library construction and may require the use of adaptors resistant to bisulphite conversion.
Hellyer et al., in paragraph [0063], teach:
[I]n some embodiments, the reactions are optimized to allow discrimination between methylated an unmethylated DNA forms, e.g., by balancing concentration and the conditions of hybridization (in particular temperature and salt concentration, as well as other factors known in the art). (Emphasis added)
Makrigiorgos, in paragraph [0007], teaches:
The temperature of the reaction mixture is then increased to the Tc, resulting in the preferential denaturation of the target-reference sequence hybridization duplexes. The Tc or critical temperature is below the T.sub.m of the reference sequence and can be determined by the methods described herein. At the Tc, the target-reference sequence duplexes (and target-target sequence duplexes only if having a lower T.sub.m than the reference sequence) are substantially denatured, whereas the target-target duplexes (if having a T.sub.m equal to or greater than the T.sub.m of the reference sequence) and the reference-reference sequence duplexes are substantially undenatured. (Emphasis added)
Makrigiorgos, in paragraphs [0052] and [0055], teach:
In other embodiments, the target sequence is methylated DNA while the reference sequence is un-methylated DNA. Alternatively, the target sequence is un-methylated DNA while the reference sequence is methylated DNA. (Emphasis added)
[0055] After the preferential denaturation of the target-reference and/or target-target sequence hybridization duplexes, the temperature of the reaction mixture is reduced so as to allow a primer pair to anneal to the target sequence. The annealed primers are then extended by a nucleic acid polymerase, thus enriching the target sequence relative to the reference sequence in the sample. (Emphasis added)
Makrigiorgos, in paragraph [0027], teach performing PCR and in paragraph [0158], teach treating the “PCR product” with an exonuclease.
The above showing is deemed to fairly suggest another limitation of claims 11, 12, 15, 16, and 19.
Applicant, at paragraph [0033] teaches:
[0033] In some embodiments of any one of the provided methods, the DSN enzyme is a DNA guided or RNA guided enzyme. In some embodiments of any one of the provided methods, the enzyme is an RNA guided enzyme, e.g., Cas9. In some embodiments of any one of the provided methods, the enzyme is a DNA guided enzyme, e.g., an Argonaute enzyme. (Emphasis added)
Van Der Oost et al., at paragraph [0052], teach using the DSN nuclease Argonaute.
In some instances, an Argonaute protein binds a DNA and cleaves the DNA. In some instances, the Argonaute protein binds a double-stranded DNA and cleaves a double-stranded DNA. (Emphasis added)
As evidenced above, Argonaute is recognized as being capable of being designed to bind and cleave any of a variety of nucleic acids. In further support of this position attention is directed to US 7,396,678 B1 (Kolodner et al.) which teaches at column 1, last paragraph, “UvrD is the helicase that appears to act in conjunction with one of the single-stranded DNA specific exonucleases to excise the unmethylated strand... (Emphasis added)
The above showing is deemed to fairly suggest limitations of claims 18, 20, and 21.
Christensen, at paragraph [0007],acknowledges the problems A-T rich sequences can provide. As stated therein:
[0007] The "A-T" rich nature of the bisulphite treated DNA provides a special challenge to primers and probes in an amplification assay due to the relatively low affinity of "A-T" rich DNAs and the difficult nature of distinguishing between a single "C" and a "T" nucleotide. (Emphasis added)
In view of the prior art recognizing “the relatively low affinity of "A-T" rich DNAs and the difficult nature of distinguishing between a single "C" and a "T" nucleotide”, it would have been obvious to one of ordinary skill in the art to remove “A-T” rich sequences from the sample prior to performing sodium bisulfite treatment, therein reducing the level of the difficulty associated with performing an amplification assay with the sodium bisulfite treated DNA.
The above showing is deemed to fairly suggest limitations of claim 22.
In view of the above presentation it would have been obvious to one of ordinary skill in the art at the time of the invention to have combined the methods of Gormley et al., Louwagie, Hellyer et al., Makrigiorgos, Van Der Oost et al., Kolodner et al., and Christensen as such would have allowed the selective amplification of sodium bisulfite nucleic acids that comprise adaptors that are resistant to sodium bisulfite, and the selective cleavage of double-stranded that is either unmethylated or methylated using exonucleases known in the art. It would have also been obvious to said ordinary artisan to have also selectively removed A-T rich sequences prior to treatment with sodium bisulfite s it was known that “"A-T" rich nature of the bisulphite treated DNA provides a special challenge to primers and probes in an amplification assay due to the relatively low affinity of "A-T" rich DNAs and the difficult nature of distinguishing between a single "C" and a "T" nucleotide.”
In view of the above analysis and in the absence of convincing evidence to the contrary, claims 11-22 are rejected under 35 U.S.C. 103 as being unpatentable over US 2009/0148842 A1 (Gormley et al.) in view of US 2012/0027870 A1 (Louwagie), US 2014/0193819 A1 (Hellyer et al.), US 2010/0203532 A1 (Makrigiorgos), US 2015/0089681 A1 (Van Der Oust et al.), US 7,396,678 B1 (Kolodner et al.), and US 2010/0068704 A1 (Christensen).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Bradley L. Sisson whose telephone number is (571)272-0751. The examiner can normally be reached Monday to Thursday, from 6:30 AM to 5 PM..
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Shen can be reached at 571-272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Bradley L. Sisson/Primary Examiner, Art Unit 1682
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