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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 08 October 2025 has been entered.
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).
Claim Rejections - 35 USC § 112, (b) / Second Paragraph
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-07.2022]:
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.”
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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, 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). (Emphasis added)
Holding and Rationale
Claims 1, 2, 6-9, 11, 14-19, 21, and 26 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 the only independent claim pending. For convenience, claim 1 is reproduced below.
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Claim 1 is indefinite with respect to what type(s) of “surface” and means of immobilization can be used.
Claim 1 is confusing as to how “universal or degenerate bases [are] arranged to oppose at least one of the remaining nucleotide positions”. (Emphasis added)
Claim 1 is confusing as to how one would necessarily know the size or length of the “single-stranded gap section” when the nucleic acid to be sequenced is unknown.
Claims 2, 6-9, 11, 14-19, 21, and 26, which depend from claim 1, fail to overcome the above identified issues and are similarly rejected.
Claims 8 and 9 are confusing as to how a nucleotide is “arranged to oppose” something.
Claim 11 is confusing as to how “the second fluorophore is tagged as a second fluorophore”.
The term “spatially arranged” in claim 17 is a relative term which renders the claim indefinite. The term “spatially arranged” is not defined by the claim, 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.
The term “fluidic channel” in claim 18 is a relative term which renders the claim indefinite. The term “fluidic channel” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite length and diameter, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
The term “surface” in claim 21 is a relative term which renders the claim indefinite. The term “surface” is not defined by the claim, 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.
For convenience, claim 26 is reproduced below.
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Claim 26 is indefinite with respect to just which “molecule[s]” is/are encompassed by the claim and can be subjected to phenotyping. Said claim is also deemed to be indefinite with respect to how one is “testing for a phenotype”.
Claim 26 is indefinite with respect to just which type(s) of molecule(s) can be “tagged with a nucleic acid molecule”.
Claim 26, step c) requires:
determining the sequence of the tagged nucleic acid molecule such that an observed phenotype is linked to the tagged nucleic acid sequence[.]
It is less than clear as to how the act of sequencing would cause a nucleic acid to be “linked”. Seemingly it may have already been linked and the act of sequencing would go to unravel just which sequence(s) has/have been linked to the (undefined) “molecule”.
Claim Rejections - 35 USC § 112, Enablement
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.
Standard for Enablement
It is well settled that in order to satisfy the enablement requirement, “the specification of a patent must teach those skilled in the art how to make and use the full scope of the claimed invention without ‘undue experimentation.’” Genentech, Inc. v. Novo Nordisk, A/S, 108 F.3d 1361, 1365 [42 USPQ2d 1001] (Fed. Cir. 1997). (Emphasis added) As set forth in the unanimous decision of the US Supreme Court in Amgen Inc, Petitioners, et al. v. Sanofi, et al. (598 US___ (May, 2023)):
Our decisions in Morse, Incandescent Lamp, and Holland Furniture reinforce the simple statutory command. If a patent claims an entire class of processes, machines, manufactures, or compositions of matter, the patent’s specification must enable a person skilled in the art to make and use the entire class. In other words, the specification must enable the full scope of the invention as defined by its claims. The more one claims, the more one must enable.
For purposes of examination, the aspect of just what constitutes the “full scope” of the claims is that which is consistent with the broadest reasonable interpretation. See MPEP 904.01 and 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 further noted that “routine experimentation is ‘not without bounds.’” Wyeth v. Abbott Laboratories 107 USPQ2d 1273, 1275, 1276 (Fed. Cir. June 2013), citing Cephalon, Inc. v. Watson Pharm., Inc., 707 F.3d 1330, 1339 [105 USPQ2d 1817] (Fed. Cir. 2013), and that what constitutes "undue experimentation" can be evaluated from the perspective of the amount of time required to enable the full scope of the invention. In support of this position, attention is directed to Cephalon at 1823, citing White Consol. Indus., Inc. v. Vega Servo-Control, Inc., 218 USPQ 961 (Fed. Cir. 1983), that work that would require 18 months to 2 years so to enable the full scope of an invention, even if routine, would constitute undue experimentation. As stated therein:
Permissible experimentation is, nevertheless, not without bounds. This court has held that experimentation was unreasonable, for example, where it was found that eighteen months to two years’ work was required to practice the patented invention. See, e.g., White Consol. Indus., Inc. v. Vega Servo-Control, Inc., 713 F.2d 788, 791 [218 USPQ 961] Fed. Cir.1983). (Emphasis added)
Claims 1-2, 6-9, 11, 14-19, 21, and 26 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.
As set forth in the last two clauses of claim 1:
wherein detecting the incidence of binding, or absence thereof, by the set of at least four fluorescently labelled oligonucleotide probes is done sequentially one after the other, such that the detection of hybridisation of each probe of the set is done in the absence of the other probes of the set;
(e) repeating steps (c) and (d) for interrogating subsequent nucleotide positions of the gap section of the immobilised nucleic acid until sufficient nucleotides of the gap section have been identified to be able to determine a sequence.
For convenience, claim 1 is reproduced below.
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Attention is directed to claim 1 at step (c), which requires:
(c) providing a set of at least four fluorescently labelled oligonucleotide probes, wherein each fluorescently labelled oligonucleotide probe is up to 20 nucleotides in length, and equal in length to the single-stranded gap section, and each probe comprising:
(i) a nucleotide X at a position arranged to oppose a nucleotide of the gap section of the immobilised nucleic acid, wherein such nucleotide is the interrogated nucleotide, and
(ii) universal or degenerate bases arranged to oppose at least one or more, or all, of the remaining nucleotide positions of the gap section[.] (Emphasis added)
Attention is also directed to claim 1, step (d). As specified therein:
(d) detecting the incidence of binding, or absence thereof, of the fluorescently labelled oligonucleotide probes with the gap section of the immobilised nucleic acid, wherein the identity of the interrogated nucleotide of the gap section of the immobilised nucleic acid is identified as the complementary base of the nucleotide X of the fluorescently labelled oligonucleotide probe that has the highest incidence of binding, wherein:
the set of at least four fluorescently labelled oligonucleotide probes are provided together and a different fluorophore is used for each of the four different oligonucleotide probes; or
wherein detecting the incidence of binding, or absence thereof, by the set of at least four fluorescently labelled oligonucleotide probes is done sequentially one after the other, such that the detection of hybridisation of each probe of the set is done in the absence of the other probes of the set[.] (Emphasis added)
As evidenced above, step (d) of claim 1 comprises multiple parts, with the last clause being optional. In support of this position attention is directed to the sue of the alternative “or”.
As evidenced above, one can employ a complete set of oligonucleotide probes which would present four labeled nucleotides (an adenine, guanine, cytosine and thymine/uracil) for each position in the 20-nucleotide gap, and then but a single nucleotide in each oligonucleotide is labeled.
It is also evident that all singular positions can be evaluated simultaneously, with all oligonucleotides having a common label for each cytosine, a common label for each guanine, a common label for each adenine, and one common label for each thymine or uracil.
It is noted that the claimed method does not require the removal of any oligonucleotide that did not hybridize to the nucleic acid being sequenced, nor does the claim specify any level of stringency.
With the use of “universal or degenerate bases” in the oligonucleotide probes, it stands to reason that the oligonucleotides probes will bind with equal specificity to both the nucleic acid of interest and the oligonucleotides that comprise universal bases.
While claim 1 does specify that “wherein the identity of the interrogated nucleotide of the gap section of the immobilised nucleic acid is identified as the complementary base of the nucleotide X of the fluorescently labelled oligonucleotide probe that has the highest incidence of binding”, such des not address how such is to be performed when there are probes in the mix that could bind at any position in the 20 nucleotide sequence, as well as to each other.
Claim 11 requires the use of FRET to identify the label associated with an oligonucleotide probe. Attention is directed to 2003/0044781 A1 (Korlach et al.), which teaches at paragraph [0105]:
FRET only reaches very short distances including about 20 nucleotides and decays at the reciprocal sixth power of distance. The excited donor molecule transfers its energy only to nearby acceptor fluorophores, which emit the spectrally resolved acceptor fluorescence of each labelled nucleotide as it is added. (Emphasis added)
As evidenced above, FRET does reach out to 20 nucleotides. Given such, it stands to reason that one would be obtaining signals for any 200 nucleotide oligonucleotide that hybridized anywhere in the 20 nucleotide gap. Given such, one would not be able to determine just which nucleotide in the 20mer had hybridized at which position, and thusly, would not be able to determine the accurate nucleotide sequence.
For convenience claim 26 is reproduced below.
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For purposes of examination the aspect of there being a nucleic acid tag on the surface of an undefined object has been construed as encompassing the sequencing of human chromosomes deposited on the surface of an object by multiple individuals.
The specification has not been found to set forth a reproducible procedure whereby the nucleotide sequence of human chromosomes could be readily determined. In support of this position it is noted that the last human chromosome was not sequenced until 23 August 2023, which is some 5 years subsequent to applicant’s effective priority date. In support of this position attention is directed to Rhie et al., “The complete sequence of a human Y chromosome”, Nature, volume 621, 14 September 2023.
In view of the above analysis and in the absence of convincing evidence to the contrary, claims 1-2, 6-9, 11, 14-19, 21, and 26 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.
Response to argument
Applicant’s representative, at pages 11-13 of the response of 08 October 2025 traverses the prior rejection. These traversals have been taken into consideration and the rejection has been modified accordingly.
Conclusion
Objections and/or rejections which appeared in the prior Office action and which have not been repeated hereinabove have been withdrawn.
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.
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/Bradley L. Sisson/Primary Examiner, Art Unit 1682