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 .
Drawings
New corrected drawings in compliance with 37 CFR 1.121(d) are required in this application because:
The margins are not of proper size in Figure(s) 1A – 14. See 37 CFR 1.84(g).
The numbering of the sheets of drawings bearing FIG(s). 1A - 14 is not in compliance with all aspects of 37 CFR 1.84(t).
Applicant is advised to employ the services of a competent patent draftsperson outside the Office, as the U.S. Patent and Trademark Office no longer prepares new drawings. The corrected drawings are required in reply to the Office action to avoid abandonment of the application. The requirement for corrected drawings will not be held in abeyance.
INFORMATION ON HOW TO EFFECT DRAWING CHANGES
Replacement Drawing Sheets
Drawing changes must be made by presenting replacement sheets which incorporate the desired changes and which comply with 37 CFR 1.84. An explanation of the changes made must be presented either in the drawing amendments section, or remarks, section of the amendment paper. 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). A replacement sheet must include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of the amended drawing(s) must not be labeled as “amended.” If the changes to the drawing figure(s) are not accepted by the examiner, applicant will be notified of any required corrective action in the next Office action. No further drawing submission will be required, unless applicant is notified.
Identifying indicia, if provided, should include the title of the invention, inventor’s name, and application number, or docket number (if any) if an application number has not been assigned to the application. If this information is provided, it must be placed on the front of each sheet and within the top margin.
Annotated Drawing Sheets
A marked-up copy of any amended drawing figure, including annotations indicating the changes made, are required by the examiner. The annotated drawing sheet(s) must be clearly labeled as “Annotated Sheet” and must be presented in the amendment or remarks section that explains the change(s) to the drawings.
Timing of Corrections
Applicant is required to submit acceptable corrected drawings within the time period set in the Office action. See 37 CFR 1.85(a). Failure to take corrective action within the set period will result in ABANDONMENT of the application.
If corrected drawings are required in a Notice of Allowability (PTOL-37), the new drawings MUST be filed within the THREE MONTH shortened statutory period set for reply in the “Notice of Allowability.” Extensions of time may NOT be obtained under the provisions of 37 CFR 1.136 for filing the corrected drawings after the mailing of a Notice of Allowability.
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, Second Paragraph / (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.
Standard for Definiteness.
Attention is directed to MPEP 2171 [R-11.2013]:
Two separate requirements are set forth in 35 U.S.C. 112(b) and pre-AIA 35 U.S.C. 112, second paragraph, namely that:
(A) the claims must set forth the subject matter that the inventor or a joint inventor regards as the invention; and
(B) the claims must particularly point out and distinctly define the metes and bounds of the subject matter to be protected by the patent grant.
The first requirement is a subjective one because it is dependent on what the inventor or a joint inventor for a patent regards as his or her invention. Note that although pre-AIA 35 U.S.C. 112, second paragraph, uses the phrase "which applicant regards as his invention," pre-AIA 37 CFR 1.41(a) provides that a patent is applied for in the name or names of the actual inventor or inventors.
The second requirement is an objective one because it is not dependent on the views of the inventor or any particular individual, but is evaluated in the context of whether the claim is definite — i.e., whether the scope of the claim is clear to a hypothetical person possessing the ordinary level of skill in the pertinent art.
Attention is directed to MPEP 2173.02 I [R-01.2024]:
During prosecution, applicant has an opportunity and a duty to amend ambiguous claims to clearly and precisely define the metes and bounds of the claimed invention. The claim places the public on notice of the scope of the patentee’s right to exclude. See, e.g., Johnson & Johnston Assoc. Inc. v. R.E. Serv. Co., 285 F.3d 1046, 1052, 62 USPQ2d 1225, 1228 (Fed. Cir. 2002) (en banc). As the Federal Circuit stated in Halliburton Energy Servs., Inc. v. M-I LLC, 514 F.3d 1244, 1255, 85 USPQ2d 1654, 1663 (Fed. Cir. 2008):
“We note that the patent drafter is in the best position to resolve the ambiguity in the patent claims, and it is highly desirable that patent examiners demand that applicants do so in appropriate circumstances so that the patent can be amended during prosecution rather than attempting to resolve the ambiguity in litigation.”
***
During examination, after applying the broadest reasonable interpretation to the claim, if the metes and bounds of the claimed invention are not clear, the claim is indefinite and should be rejected. Packard, 751 F.3d at 1310 (“[W]hen the USPTO has initially issued a well-grounded rejection that identifies ways in which language in a claim is ambiguous, vague, incoherent, opaque, or otherwise unclear in describing and defining the claimed invention, and thereafter the applicant fails to provide a satisfactory response, the USPTO can properly reject the claim as failing to meet the statutory requirements of § 112(b).”); Zletz, 893 F.2d at 322, 13 USPQ2d at 1322.
Attention is also directed to MPEP 2173.02 III B [R-01-2024], which states in part:
To comply with 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph, applicants are required to make the terms that are used to define the invention clear and precise, so that the metes and bounds of the subject matter that will be protected by the patent grant can be ascertained. See MPEP § 2173.05(a), subsection I. It is important that a person of ordinary skill in the art be able to interpret the metes and bounds of the claims so as to understand how to avoid infringement of the patent that ultimately issues from the application being examined. See MPEP § 2173.02, subsection II (citing Morton Int ’l, Inc. v. Cardinal Chem. Co., 5 F.3d 1464, 1470 (Fed. Cir. 1993)); see also Halliburton Energy Servs., 514 F.3d at 1249, 85 USPQ2d at 1658 (“Otherwise, competitors cannot avoid infringement, defeating the public notice function of patent claims.”). Examiners should bear in mind that “[a]n essential purpose of patent examination is to fashion claims that are precise, clear, correct, and unambiguous. Only in this way can uncertainties of claim scope be removed, as much as possible, during the administrative process.” Zletz, 893 F.2d at 322, 13 USPQ2d at 1322 [Fed. Cir. 1989]. (Emphasis added)
Attention is also directed to MPEP 2173.04 [R-10-2019], which states in part:
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).
Holding and Rationale
Claims 1-20 are 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 1 is indefinite with respect to what constitutes the metes and bounds of “double-stranded polynucleotide”, “attached”, “a first invasion primer”, “a second invasion primer”, “a first sequencing primer” and “a second sequencing primer”. In support of this position it is noted that it is unclear as to whether the “double-stranded polynucleotide” is artificial or naturally occurring, and if the later, it is unclear as what is/are the source(s)/organism(s) of the “double-stranded polynucleotide”. It is also unclear if the “double-stranded polynucleotide” is limited to that which was known at the time of filing or whether it encompasses sequences that had not yet been discovered. It is also unclear if the “double-stranded polynucleotide” is linear or circular in design, and if linear, that it has folded back upon itself and forming a double-stranded region/component
It is also unclear if the “double-stranded polynucleotide” can be an oligonucleotide.
It is also unclear as to what constitutes the metes and bounds of “a first invasion primer”, “a second invasion primer”, “a first sequencing primer” and “a second sequencing primer”. As presently worded, the claim does not recite any length or range of lengths for these four primers. It is also unclear as to what secondary structure, if any, each of these fours primers have. It is also unclear as to what is being invaded by an “invasion primer”. Attention is directed to US 2003/0099950 A1 (Hanna), which teaches the following in paragraph [0154]:
In one embodiment, the primers are less than about 25 nucleotides in length, usually from about 1 to about 10 nucleotides in length, and preferably about 2 to 3 nucleotides in length. It may be desirable to modify the nucleotides or phosphodiester linkages in one or more positions of the primer. Examples of such modifications include, but are not limited to, fluorescent molecules and energy transfer dyes (such as, fluorescein, aedans, coumarine, bodipy dyes, and rhodamine based dyes), fluorescent quencher molecules (for example, Dabcyl), proteins, peptides, amino linkers, or amino acid based molecules (for example polyhistidine), modified bases and modified and unmodified base analogs, peptide nucleic acids (PNAs), methylphosphonates, radioactive labels, terminal phosphates, 3' glyceryl, other carbohydrate based molecules, fatty acid derived molecules, carbon spacer molecules, electrochemiluminescent labels, lanthanide labels, avidin and its derivatives (for example, streptavidin, Neutravidin, etc.), biotin, steroid molecules (such as Digoxygenin), thiol linkages, ferritin labels, and the like. (Emphasis added)
Attention is also directed to US 5,439,793 (Rose et al.), which teaches at column 21, second paragraph:
The polynucleotide primer is preferably 10 to 100 nucleotides in length.
Attention is also directed to US 2005/0142596 A1 (Krolewski et al.), which teaches at paragraph [0030]:
[0030] In some embodiments, the probe or primer is 500 nucleotides or less in length, e.g., about, 400, 300, 250, 200, or 100 nucleotides or less in length.
With regard to the term “attached”, it is unclear as to the type of bonding, e.g., hydrogen or covalent, is occurring between which molecules.
Claim 1 is indefinite with respect to what level of stringency or specificity under which the act of “hybridizing” occurs.
Claim 1 is indefinite with respect to how one is to perform the act of “generating a first sequencing read” and “generating a second sequencing read”.
Claims 2 and 5-17, which depend from claim 1, fail to overcome each of the above identified issues and are similarly rejected.
Claims 2 and 3 are indefinite with respect to what means, e.g., a detectable moiety, is/are being detected and thereby allows for performance of the step requiring “detecting the one or more incorporated nucleotides”. It is also unclear if the detection is performed after all nucleotides had been incorporated into the primer, or whether they are being detected as each nucleotide is incorporated. As presently worded, the claims do not recite any limitation of there being any detectable moiety. Given such absence, it is less than clear as to how one is to perform this step of “detecting the one or more incorporated nucleotides”.
Claim 3 is indefinite with respect to what constitutes the metes and bounds of “attached”, “a first invasion primer”, “a second invasion primer”, “a first sequencing primer” and “a second sequencing primer”. It is less than clear as to what type(s) of bonds, e.g., covalent or hydrogen, and whether any intervening molecule, e.g., a linker of some type, is/are being used to “attach the first strand and second strand to a solid support”. It is less than clear as to what constitutes the metes and bounds of the first and second “invasion primer” and the first and second “sequencing primer”. It is noted that “the second invasion primer” and the “first sequencing primer” are each supposed to hybridize to the “first strand”. It is less than clear as to just what is/are the differences between the “the second invasion primer” and the “first sequencing primer”. Similar issues exist with regard to the “first invasion primer” and the “second sequencing primer” as both are to hybridize to the “second strand”. With four different primers hybridizing to two strands, it is unclear if any pair of primers that hybridize to the same strand, are to hybridize to the same nucleotide sequence. It is also unclear as to how one is to detect the order of nucleotides that were added to any primer, much less determine the order of nucleotides after all had been incorporated to each of the four primers.
Claim 15 is indefinite with respect to what constitutes the metes and bounds for each of “locked nucleic acids (LNAs), Bis-locked nucleic acids (bisLNAs), twisted intercalating nucleic acids (TINAs), bridged nucleic acids (BNAs), 2'-O-methyl RNA:DNA chimeric nucleic acids, minor groove binder (MGB) nucleic acids, morpholino nucleic acids, CS-modified pyrimidine nucleic acids, peptide nucleic acids (PNAs), [and] phosphorothioate nucleotides”. Acknowledgement is made of the description found at paragraph [004] of the specification. As found therein, non-limiting descriptions are to be found in various non-patent literature articles. It is noted with particularity that essential material may not be incorporated by reference to non-patent literature.1
The term “more” in claims 2, 3, 6, 10, 16, and 17 is a relative term which renders the claims indefinite. The term “more” is not defined by the claims, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
Claim 4, which depends from claim 3, fails to overcome each of the above identified issues and is similarly rejected.
Response to traversal
Applicant’s representative, at pages 9-12 of the response of 13 November 2025, hereinafter the response, traverses the rejection of claims under 35 USC 112(b). At page 9 of the response said representative asserts:
The Examiner alleges that claim 1 is indefinite as to "double-stranded polynucleotide," "attached," "a first invasion primer," "a second invasion primer," "a first sequencing primer," and "a second sequencing primer." Applicant disagrees. The specification defines "polynucleotide," "nucleic acid," "strand," and related terms as interchangeable and encompassing polymers of deoxyribonucleotides or ribonucleotides and their analogs, including primers and templates. A double-stranded polynucleotide is two such strands in duplex. See [0033]. "Attached," "bind," and "bound" carry their plain meanings and include direct or indirect association through covalent or non-covalent interactions, including via intermediates, and the claims require that both strands are attached to a solid support. See [0063]. A "primer" is a polynucleotide that hybridizes to a template, can be bound by a polymerase, and is extendable in a template-directed process, with exemplar lengths and the possibility of attachment to a solid support. See [0034]. An "invasion primer" is a primer capable of hybridizing to one strand of a duplex via strand invasion, and an "invasion strand" is the extended product of that primer. The specification identifies suitable chemistries and strand-displacing polymerases. See [0035] to [0037]. A "sequencing primer" is a primer used to initiate sequencing and therefore falls within the primer definition in [0034]. Each term has a single, art-recognized meaning as used and is supported by the application as filed. The rejection does not articulate any competing reasonable interpretation, contrary to MPEP 2173.02. (Emphasis in original)
The Examiner alleges that claim 1 is indefinite because the level of stringency or specificity for "hybridizing" is not recited. Applicant disagrees. "Hybridize" is defined as annealing based on sequence complementarity, and the specification identifies controlling parameters including temperature, ionic strength, length, and degree of complementarity, with exemplary temperature ranges and buffer adjustments. See [0079], for example. Selection of particular conditions is an implementation detail and does not create ambiguity. The rejection does not identify more than one reasonable meaning for "hybridizing," as required by MPEP 2173.02.
The above arguments have been considered and have not been found persuasive. 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)
As set forth in the body of the rejection the issue of primer length was presented. In support of this position attention is directed to US 2003/0099950 A1 (Hanna), which teaches the following in paragraph [0154]:
In one embodiment, the primers are less than about 25 nucleotides in length, usually from about 1 to about 10 nucleotides in length, and preferably about 2 to 3 nucleotides in length. It may be desirable to modify the nucleotides or phosphodiester linkages in one or more positions of the primer. Examples of such modifications include, but are not limited to, fluorescent molecules and energy transfer dyes (such as, fluorescein, aedans, coumarine, bodipy dyes, and rhodamine based dyes), fluorescent quencher molecules (for example, Dabcyl), proteins, peptides, amino linkers, or amino acid based molecules (for example polyhistidine), modified bases and modified and unmodified base analogs, peptide nucleic acids (PNAs), methylphosphonates, radioactive labels, terminal phosphates, 3' glyceryl, other carbohydrate based molecules, fatty acid derived molecules, carbon spacer molecules, electrochemiluminescent labels, lanthanide labels, avidin and its derivatives (for example, streptavidin, Neutravidin, etc.), biotin, steroid molecules (such as Digoxygenin), thiol linkages, ferritin labels, and the like. (Emphasis added)
Attention is also directed to US 5,439,793 (Rose et al.), which teaches at column 21, second paragraph:
The polynucleotide primer is preferably 10 to 100 nucleotides in length.
Attention is also directed to US 2005/0142596 A1 (Krolewski et al.), which teaches at paragraph [0030]:
[0030] In some embodiments, the probe or primer is 500 nucleotides or less in length, e.g., about, 400, 300, 250, 200, or 100 nucleotides or less in length.
As evidenced above, there is not a single art-recognized length for primers. The claims do not recite such a limitation. Consequently, it is not readily apparent as to what length, or range of lengths of primers, are encompassed by the claims.
With regard to the term “attached”, it is unclear as to the type of bonding, e.g., hydrogen or covalent, is occurring between which molecules.
As set forth above, claim 1 is indefinite with respect to what level of stringency or specificity under which the act of “hybridizing” occurs. While argument has been presented that “Selection of particular conditions is an implementation detail and does not create ambiguity.”, the aspect of just which conditions, or range of conditions do speak directly to how the claimed assay is to be performed, and whether the conditions may impart issues of inoperability. In support of this position attention is directed to US 2014/0038181 A1 (Lebedev et al.), at paragraph [0271], teach:
[0271] As used herein, the term "stringent hybridization condition," "high stringency hybridization condition" or "stringent conditions" refers to hybridization conditions which do not allow for hybridization of two nucleic acids sequences which are not completely complementary. As used herein, the term "non-stringent hybridization condition" or "low stringency hybridization condition" or "low stringent conditions" refers to hybridization conditions which allow for hybridization of two nucleic acids sequences which are not completely complementary or contain mismatch nucleotides at one or more position. (Emphasis added)
By not knowing the stringency of the assay, one is not informed of the potentiality of primers not hybridizing across their full length to the intended target, but rather at just the last 1, 2 or 3 nucleotides, and therein allowing for the production of a primer extension product (sequencing extension; sequencing reads) that is not of the intended target.
At page 10 of the response argument is presented that “Each dependent claim increases clarity.” While the dependent claims do present additional limitations, they have not been found to resolve all issues of record. For example, none of the claims, be it independent of dependent, clarify the lengths of primers and the stringency of the hybridization conditions.
At page 10, bridging to page 11 of the response, said representative asserts:
The Examiner alleges that claims 2 and 3 are indefinite because the claims do not identify what means, for example a detectable moiety, is being detected when "detecting the one or more incorporated nucleotides." Applicant disagrees. The claims require detection sufficient to identify each incorporated nucleotide, which is the field standard for base calling from incorporation events and which is expressly tied to the generation of sequencing reads. See [0076]. MPEP 2173.02 makes clear that definiteness turns on clarity of scope, not on prescribing a single label or detector when the boundary is the identification of each incorporated base. The rejection does not identify any competing reasonable interpretation.
The above arguments have been considered and have not been found persuasive. 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)
In the present case it is less than clear as to just what about the nucleotides is being detected so as to enable claim 3, steps (D) and (F)- “detecting the one or more incorporated nucleotides so as to identify each incorporated nucleotide”. It is further noted that the claims do not require the removal of any label, while at the same time encompassing the detection of each and every incorporated nucleotide once they have all been incorporated into the sequencing primer extension product. It is less than clear as to just how such is to be achieved.
At page 11 of the response said representative traverses the rejection of claim 15 under 35 USC 112(b). As is asserted to therein:
The Examiner alleges that claim 15 is indefinite as to the listed chemistries, including locked nucleic acids, bis-locked nucleic acids, twisted intercalating nucleic acids, bridged nucleic acids, 2'-O-methyl RNA:DNA chimeric nucleic acids, minor groove binder nucleic acids, morpholino nucleic acids, C5-modified pyrimidine nucleic acids, peptide nucleic acids, and phosphorothioate nucleotides, and raises an issue regarding incorporation by reference. Applicant disagrees. These are names of the art with objective, settled meanings to skilled artisans, and the specification situates such chemistries as examples of primers with higher binding affinity used for strand invasion. See [0035]. Under MPEP 2173.04, breadth across known species does not render a claim indefinite where the scope is clear. Definiteness turns on ordinary meaning in the art, not on incorporation of external literature. The rejection identifies no alternative reasonable meaning for any listed class. (Emphasis added)
This argument has been fully considered and has not been found persuasive. Attention is directed to MPEP 2145 I [R-01.2024].
An argument by the applicant is not evidence unless it is an admission, in which case, an examiner may use the admission in making a rejection. See MPEP § 2129 and § 2144.03 for a discussion of admissions as prior art.
Arguments presented by applicant cannot take the place of evidence in the record. See In re De Blauwe, 736 F.2d 699, 705, 222 USPQ 191, 196 (Fed. Cir. 1984); In re Schulze, 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965); In re Geisler, 116 F.3d 1465, 43 USPQ2d 1362 (Fed. Cir. 1997) ("An assertion of what seems to follow from common experience is just attorney argument and not the kind of factual evidence that is required to rebut a prima facie case of obviousness."). See MPEP § 716.01(c) for examples of applicant statements which are not evidence and which must be supported by an appropriate affidavit or declaration
Attention is also 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)
In the present case no declaration has been filed which presents evidence that “These are names of the art with objective, settled meanings to skilled artisans…” and that it is clear as to just which species are covered.
In view of he above analysis and in the absence of convincing evidence to the contrary, claims 1-20 are 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 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.
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.
Standard for Obviousness.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) 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.
Attention is directed to In re Jung, 98 USPQ2d 1174, 1178 (Fed. Cir. 2011) wherein is stated:
There has never been a requirement for an examiner to make an on-the-record claim construction of every term in every rejected claim and to explain every possible difference between the prior art and the claimed invention in order to make out a prima facie rejection. This court declines to create such a burdensome and unnecessary requirement. “[Section 132] does not mandate that in order to establish prima facie anticipation, the PTO must explicitly preempt every possible response to a section 102 rejection. Section 132 merely ensures that an applicant at least be informed of the broad statutory basis for the rejection of his claims, so that he may determine what the issues are on which he can or should produce evidence.” Chester, 906 F.2d at 1578 (internal citation omitted). As discussed above, all that is required of the office to meet its prima facie burden of production is to set forth the statutory basis of the rejection and the reference or references relied upon in a sufficiently articulate and informative manner as to meet the notice requirement of § 132. As the statute itself instructs, the examiner must “notify the applicant,” “stating the reasons for such rejection,” “together with such information and references as may be useful in judging the propriety of continuing prosecution of his application.” 35 U.S.C. § 132.
Attention is directed to the decision in KSR International Co. v. Teleflex Inc., 82 USPQ2d 1385 (U.S. 2007):
When there is a design need or market pressure to solve a problem and there are a finite number of identified, predictable solutions, a person of ordinary skill in the art has good reason to pursue the known options within his or her technical grasp. If this leads to the anticipated success, it is likely the product not of innovation but of ordinary skill and common sense.
It is further noted that prior art is not limited to the four corners of the documentary prior art being applied. Prior art includes both the specialized understanding of one of ordinary skill in the art, and the common understanding of the layman. It includes “background knowledge possessed by a person having ordinary skill in the art. . . [A] court can take account of the inferences and creative steps that a person of ordinary skill in the art would employ.” KSR at 1396.
Suggestion, teaching or motivation does not have to be explicit and “may be found in any number of sources, including common knowledge, the prior art as a whole or the nature of the problem itself’” Pfizer, Inc. v. Apotex, Inc. 480 F.3d 1348, 82 USPQ2d 1321 (Fed. Cir. 2007) citing Dystar Textilfarben GMBH v. C. H. Patrick Co., 464 F.3d 1356 (Fed. Cir. 2006).
Holding and Rationale
Claim(s) 1-20 are rejected under 35 U.S.C. 103 as being unpatentable over US 2021/0277461 A1 (Glezer et al.) and US 2018/0201924 A1 (Peter et al.).
Glezer et al., in the abstract, teach:
Provided herein are methods for sequencing both strands of a double stranded nucleic acid fragment that improves fidelity and accuracy of a sequence determination compared to traditional next generation sequencing methods. Compositions and kits for use in the methods are also provided. (Emphasis added)
Glezer et al., in paragraph [0070], [0071], [0073], and [0094], teach:
In some embodiments, a sequencing process described herein comprises contacting a template and an annealed primer with a suitable polymerase under conditions suitable for polymerase extension and/or sequencing. The sequencing methods are preferably carried out with the target polynucleotide arrayed on a solid substrate. Multiple target polynucleotides can be immobilized on the solid support through linker molecules, or can be attached to particles, e.g., microspheres, which can also be attached to a solid substrate. In embodiments, the solid substrate is in the form of a chip, a bead, a well, a capillary tube, a slide, a wafer, a filter, a fiber, a porous media, or a column. In embodiments, the solid substrate is gold, quartz, silica, plastic, glass, diamond, silver, metal, or polypropylene. In embodiments, the solid substrate is porous. (Emphasis added)
[0071] As used herein, the terms “solid support” and “substrate” and “solid surface” refers to discrete solid or semi-solid surfaces to which a plurality of primers may be attached. A solid support may encompass any type of solid, porous, or hollow sphere, ball, cylinder, or other similar configuration composed of plastic, ceramic, metal, or polymeric material (e.g., hydrogel) onto which a nucleic acid may be immobilized (e.g., covalently or non-covalently). A solid support may comprise a discrete particle that may be spherical (e.g., microspheres) or have a non-spherical or irregular shape, such as cubic, cuboid, pyramidal, cylindrical, conical, oblong, or disc-shaped, and the like. Solid supports in the form of discrete particles may be referred to herein as “beads,” which alone does not imply or require any particular shape. A bead can be non-spherical in shape. A solid support may further comprise a polymer or hydrogel on the surface to which the primers are attached (e.g., the splint primers are covalently attached to the polymer, wherein the polymer is in direct contact with the solid support). Exemplary solid supports include, but are not limited to, glass and modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethanes, Teflon™, cyclic olefin copolymers, polyimides etc.), nylon, ceramics, resins, Zeonor, silica or silica-based materials including silicon and modified silicon, carbon, metals, inorganic glasses, optical fiber bundles, photopatternable dry film resists, UV-cured adhesives and polymers. The solid supports for some embodiments have at least one surface located within a flow cell. The solid support, or regions thereof, can be substantially flat. The solid support can have surface features such as wells, pits, channels, ridges, raised regions, pegs, posts or the like. The term solid support is encompassing of a substrate (e.g., a flow cell) having a surface comprising a polymer coating covalently attached thereto. In embodiments, the solid support is a flow cell. The term “flow cell” as used herein refers to a chamber including a solid surface across which one or more fluid reagents can be flowed. Examples of flow cells and related fluidic systems and detection platforms that can be readily used in the methods of the present disclosure are described, for example, in Bentley et al., Nature 456:53-59 (2008).
[0073] As used herein, the term “sequencing cycle” is used in accordance with its plain and ordinary meaning and refers to incorporating one or more nucleotides (e.g., nucleotide analogues) to the 3′ end of a polynucleotide with a polymerase, and detecting one or more labels that identify the one or more nucleotides incorporated. The sequencing may be accomplished by, for example, sequencing by synthesis, pyrosequencing, and the like. In embodiments, a sequencing cycle includes extending a complementary polynucleotide by incorporating a first nucleotide using a polymerase, wherein the polynucleotide is hybridized to a template nucleic acid, detecting the first nucleotide, and identifying the first nucleotide. In embodiments, to begin a sequencing cycle, one or more differently labeled nucleotides and a DNA polymerase can be introduced.
[0094] In some embodiments, a double stranded nucleic comprises two complementary nucleic acid strands. In certain embodiments, a double stranded nucleic acid comprises a first strand and a second strand which are complementary or substantially complementary to each other. A first strand of a double stranded nucleic acid is sometimes referred to herein as a forward strand and a second strand of the double stranded nucleic acid is sometime referred to herein as a reverse strand. In some embodiments, a double stranded nucleic acid comprises two opposing ends. Accordingly, a double stranded nucleic acid often comprises a first end and a second end. An end of a double stranded nucleic acid may comprise a 5′-overhang, a 3′-overhang or a blunt end.
Glezer et al., in paragraphs [0174], [0269], teach:
[0174] In embodiments, generating the blocking strand includes extending the invasion primer by incorporating one or more nucleotides (e.g., dNTPs) using Bst large fragment (Bst LF) polymerase, Bst2.0 polymerase, Bsu polymerase, SD polymerase, Vent exo-polymerase, Phi29 polymerase, or a mutant thereof. (Emphasis added)
[0269] Another method is the use of an insertion primer complementary to a portion of the 5′ region of the double stranded portion of a hairpin adapter (an “invasion primer”), within a polynucleotide duplex including a double stranded nucleic acid of interest ligated to a Y-adapter and the hairpin adapter. (Emphasis added)
The aspect of how many times an “invasion primer” is used/repeated is deemed to be an obvious design choice. (Claim 17)
The aspect of having the first and second strand of the polynucleotide bound to a solid support via linkage via the 5’ end (claim 20) is deemed to be an obvious design choice.
The aspect of denaturing all or a portion of one strand from the other is recognized as being inherent to amplification reactions where one must first render the target nucleic acid single stranded so that the primer(s) can bind and then be extended/elongated via the incorporation of nucleotides, including modified nucleotides.
Glezer et al., in paragraphs [0133] and [0175], lists denaturants that can be used at various points of the method, including amplification (applicant’s “invasion cycles). The chemical denaturants identified are:
[0133] In embodiments, amplifying includes incubation in a denaturant. In embodiments, the denaturant is acetic acid, ethylene glycol, hydrochloric acid, nitric acid, formamide, guanidine, sodium salicylate, sodium hydroxide, dimethyl sulfoxide (DMSO), propylene glycol, urea, or a mixture thereof. In embodiments, the denaturant is an additive that lowers a DNA denaturation temperature. In embodiments, the denaturant is betaine, dimethyl sulfoxide (DMSO), ethylene glycol, formamide, glycerol, guanidine thiocyanate, 4-methylmorpholine 4-oxide (NMO), or a mixture thereof. In embodiments, the denaturant is betaine, dimethyl sulfoxide (DMSO), ethylene glycol, formamide, glycerol, guanidine thiocyanate, or 4-methylmorpholine 4-oxide (NMO). (Emphasis added)
[0175] In embodiments, the reaction conditions for the extension cycles include incubation in a denaturant. In embodiments, the denaturant is a buffered solution including betaine, dimethyl sulfoxide (DMSO), ethylene glycol, formamide, glycerol, guanidine thiocyanate, 4-methylmorpholine 4-oxide (NMO), or a mixture thereof. In embodiments, the denaturant is a buffered solution including betaine, dimethyl sulfoxide (DMSO), ethylene glycol, formamide, or a mixture thereof. In embodiments, the denaturant is a buffered solution including about 0% to about 50% dimethyl sulfoxide (DMSO); about 0% to about 50% ethylene glycol; about 0% to about 20% formamide; or about 0 to about 3M betaine, or a mixture thereof. In embodiments, the reaction conditions include incubation in a denaturant, wherein the denaturant is a buffered solution including about 15% to about 50% dimethyl sulfoxide (DMSO); about 15% to about 50% ethylene glycol; about 10% to about 20% formamide; or about 0 to about 3M betaine, or a mixture thereof.
The above showing is deemed to fairly suggest limitations of claims 13-14.
Glezer et al., in paragraph [0138], teach the inclusion and use of cleavage sites in primers. As disclosed therein:
[0138] Any suitable enzymatic, chemical, or photochemical cleavage reaction may be used to cleave the cleavage site. The cleavage reaction may result in removal of a part or the whole of the strand being cleaved. Suitable cleavage means include, for example, restriction enzyme digestion, in which case the cleavage site is an appropriate restriction site for the enzyme which directs cleavage of one or both strands of a duplex template; RNase digestion or chemical cleavage of a bond between a deoxyribonucleotide and a ribonucleotide, in which case the cleavage site may include one or more ribonucleotides; chemical reduction of a disulfide linkage with a reducing agent (e.g., THPP or TCEP), in which case the cleavage site should include an appropriate disulfide linkage; chemical cleavage of a diol linkage with periodate, in which case the cleavage site should include a diol linkage; generation of an abasic site and subsequent hydrolysis, etc. In embodiments, the cleavage site is included in the surface immobilized primer (e.g., within the polynucleotide sequence of the primer). In embodiments, one strand of the double-stranded amplification product (or the surface immobilized primer) may include a diol linkage which permits cleavage by treatment with periodate (e.g., sodium periodate). It will be appreciated that more than one diol can be included at the cleavage site. One or more diol units may be incorporated into a polynucleotide using standard methods for automated chemical DNA synthesis. (Emphasis added)
The selection of number and types of cleavage sites, and the sequence(s) to comprise same is deemed to be an obvious design choice. (Claim 6)
While Glezer et al., teaches using invasive primers, they have not been found to teach using invasion primers that comprise one or more locked nucleic acids.
Peter et al., at paragraph [0075], teaches
Methods of modulating the effect of PCR suppression or enabling primer invasion into a hairpin portion of a duplex are known in the art, and include techniques such as adjusting primer concentration, adjusting primer sequence, using modified bases of nucleotides such as unstructured nucleic acids or Locked Nucleic acids, adjusting salt concentration, increasing template length, toehold primers as described in J Am Chem Soc. 2013 Apr. 17; 135(15):5612-9, and the like. (Emphasis added)
The above showing is deemed to fairly suggest limitations of claim 16.
The aspect of performing an amplification reaction such as polymerase chain reaction (PCR) is recognized as comprising the amplification of both strands, which can be performed sequentially or simultaneously. Given such, the aspect of “extending the first invasion primer hybrized to the second strand and extending the second invasion primer hybridized to the first strand is performed sequentially” is deemed to be a matter of obvious design choice. (Claim 7)
In view of the above presentation, the claimed methods of sequencing a double-stranded polynucleotide is deemed to be obvious in view of the teachings of US 2021/0277461 A1 (Glezer et al.) and US 2018/0201924 A1 (Peter et al.). Given such, and in the absence of convincing evidence to the contrary, claims 1-20 are rejected under 35 U.S.C. 103 as being unpatentable over US 2021/0277461 A1 (Glezer et al.) and US 2018/0201924 A1 (Peter et al.).
Response to traversal
Applicant’s representative, at pages 12-14 of the response traverses the rejection of claims under 35 USC 103(a). At page 13 of the response said representative asserts:
Dual immobilization is not taught or suggested. The independent claims require "wherein the first strand and second strand are both attached to a solid support." Glezer does not disclose immobilizing both complementary strands of the same duplex. To the contrary, Glezer illustrates attachment of only one strand, with the opposite strand free in solution. See, for example, Glezer FIG. 15B and FIG. 18A. The Office identifies no teaching or suggestion to modify Glezer to immobilize both strands, and offers no rationale with rational underpinning for doing SO. Every limitation must be taught or suggested.
The above argument has been considered and has not been found persuasive. Contrary to assertions by applicant, the prior art does teach sequencing both strands of a double stranded polynucleotide and that multiple nucleic acids can be on a common support. In support of this position attention is directed to Glezer et al., in the abstract, teach:
Provided herein are methods for sequencing both strands of a double stranded nucleic acid fragment that improves fidelity and accuracy of a sequence determination compared to traditional next generation sequencing methods. Compositions and kits for use in the methods are also provided. (Emphasis added)
Glezer et al., in paragraph [0070], [0071], [0073], and [0094], teach:
In some embodiments, a sequencing process described herein comprises contacting a template and an annealed primer with a suitable polymerase under conditions suitable for polymerase extension and/or sequencing. The sequencing methods are preferably carried out with the target polynucleotide arrayed on a solid substrate. Multiple target polynucleotides can be immobilized on the solid support through linker molecules, or can be attached to particles, e.g., microspheres, which can also be attached to a solid substrate. In embodiments, the solid substrate is in the form of a chip, a bead, a well, a capillary tube, a slide, a wafer, a filter, a fiber, a porous media, or a column. In embodiments, the solid substrate is gold, quartz, silica, plastic, glass, diamond, silver, metal, or polypropylene. In embodiments, the solid substrate is porous. (Emphasis added)
Given such explicit teachings, the obvious design choice is fairly applicable.
In view of the above presentation and in the absence of convincing evidence to the contrary, claims 1-20 are rejected under 35 U.S.C. 103 as being unpatentable over US 2021/0277461 A1 (Glezer et al.) and US 2018/0201924 A1 (Peter et al.).
Conclusion
Objections and/or rejections which appeared in the prior Office action and which have not been repeated hereinabove have been withdrawn.
THIS ACTION IS MADE FINAL. 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 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.
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, 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.
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.
/Bradley L. Sisson/Primary Examiner, Art Unit 1682
1 Attention is directed to 37 CFR 1.57(d), which sates in part:
(d) "Essential material" may be incorporated by reference, but only by way of an incorporation by reference to a U.S. patent or U.S. patent application publication, which patent or patent application publication does not itself incorporate such essential material by reference. "Essential material" is material that is necessary to:
(1) Provide a written description of the claimed 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 set forth the best mode contemplated by the inventor of carrying out the invention as required by 35 U.S.C. 112(a);
(2) Describe the claimed invention in terms that particularly point out and distinctly claim the invention as required by 35 U.S.C. 112(b); or
(3) Describe the structure, material, or acts that correspond to a claimed means or step for performing a specified function as required by 35 U.S.C. 112(f). (Emphasis added)
(e) Other material ("Nonessential material") may be incorporated by reference to U.S. patents, U.S. patent application publications, foreign patents, foreign published applications, prior and concurrently filed commonly owned U.S. applications, or non-patent publications. An incorporation by reference by hyperlink or other form of browser executable code is not permitted.