DETAILED ACTION
Election/Restrictions
Applicant’s election of species (1) (the detectably labeled probes comprise hydrolysis probes, see claim 28) and species (4) (the signal is detected using a detection apparatus comprising a photomultiplier tube, see claims 34-36) in the reply filed on August 28, 2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)). Claims 21-37 will be examined.
Specification
The disclosure is objected to because of the following informalities: since this application claims priority for provisional application 61/887,103 and US application 14/505,974 (now US Patent No. 11,901,041), applicant may consider to put these applications to the first paragraph of the specification.
Appropriate correction is required.
Claim Objections
Claim 21 is objected to because of the following informalities: (1) “a sample” in treating step should be “the sample”; (2) “the sample” in partitioning step should be “the digested sample”; (3) “performing amplification” should be “performing amplification reactions”; (4) “signal” in detecting step should be “a signal” or “signals”; and (5) “a quantity of the target nucleic acids that was present in the sample” should be “a quantity of the target nucleic acid that is present in the sample”.
Claim 23 is objected to because of the following informality: “the target nucleic acid” should be “the non-target nucleic acid” in view of claim 21.
Claim 33 is objected to because of the following informality: “each droplet” should be “each of the aqueous droplets”.
Claim 35 is objected to because of the following informality: the word “was” should be “is”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
New Matter
Claims 21-31 and 34-37 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 written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Newly added independent claim 21 contains a limitation “performing amplification in the compartments with detectably-labeled probes specific to the locus”. Although the specification describes that “[T]he amplified product in each droplet may be detected by, for example, a hydrolysis probe-based assay”, “[I]n one aspect, the invention provides droplets containing a single nucleic acid template or fewer, amplification reagents, and one or more detectable probes. The amplification reagents may include multiplexed PCR primers that along with the detectable probes may be specific to the modification-dependent target(s), reference target(s), or control nucleic acid(s). Methods of the invention also provide for detecting the nucleic acid template by forming such droplets and amplifying the nucleic acid templates using droplet based digital amplification” and “[T]raditional digital PCR methods involve the use of a single labeled probe specific for an individual target. FIG. 5 is a schematic depicting one-color detection of a target dsDNA sequence using droplet based digital PCR. As shown in Panel A of FIG. 5, a template DNA is amplified with a forward primer (F1) and a reverse primer (R1). Probe (P1) labeled with a fluorophore of color 1 binds to the target genetic sequence (target 1). Microdroplets are made of diluted solution of template DNA under conditions of limiting or terminal dilution. Droplets containing the target sequence emit fluorescence and are detected by laser (Panels B and C). The number of microcapsules either containing or not containing the target sequence is shown in a histogram (D) and quantified (E)” (see paragraphs [0012], [0033] and [0100] of US 2024/0185950 A1, which is US publication of this instant case), page 2, line 27 to page 3, line 18, page 13, lines 7-17, page 18, lines 13-17, page 26, lines 11-13, page 31, page 32, lines 3-8, page 33, lines 16-20, page 36, lines 18-21 and page 40, line 4 to page 42, line 14 of the specification suggested by applicant do not describe such limitation in claim 21 since the specification only describes that an amplification in the presence of detectably-labeled probes specific to the locus is performed only in droplets (see paragraphs [0033] and [0100]).
MPEP 2163.06 notes “If new matter is added to the claims, the examiner should reject the claims under 35 U.S.C. 112, first paragraph - written description requirement. In re Rasmussen, 650 F.2d 1212, 211 USPQ 323 (CCPA 1981).” MPEP 2163.02 teaches that “Whenever the issue arises, the fundamental factual inquiry is whether a claim defines an invention that is clearly conveyed to those skilled in the art at the time the application was filed...If a claim is amended to include subject matter, limitations, or terminology not present in the application as filed, involving a departure from, addition to, or deletion from the disclosure of the application as filed, the examiner should conclude that the claimed subject matter is not described in that application.” MPEP 2163.06 further notes “When an amendment is filed in reply to an objection or rejection based on 35 U.S.C. 112, first paragraph, a study of the entire application is often necessary to determine whether or not “new matter” is involved. Applicant should therefore specifically point out the support for any amendments made to the disclosure” (emphasis added).
Scope of Enablement
Claims 21-37 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for treating a sample comprising (i) target nucleic acid comprising a locus and (ii) non- target nucleic acid comprising the locus with a methylation-sensitive restriction enzyme (MSRE) to selectively digest only the non-target nucleic acid, does not reasonably provide enablement for determining a quantity of the target nucleic acids that is present in the sample by detecting any kind of signal from detectably-labeled probes using the methods recited in claims 21-37. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
Factors to be considered in determining whether a disclosure meets the enablement requirement of 35 USC 112, first paragraph, have been described by the court in In re Wands, 8 USPQ2d 1400 (CA FC 1988). Wands states at page 1404,
“Factors to be considered in determining whether a disclosure would require undue experimentation have been summarized by the board in Ex parte Forman. They include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims.”
The Nature of The Invention
The claims are drawn to a method for analysis of nucleic acid. The invention is a class of invention which the CAFC has characterized as “the unpredictable arts such as chemistry and biology.” Mycogen Plant Sci., Inc. v. Monsanto Co., 243 F.3d 1316, 1330 (Fed. Cir. 2001).
The Breadth of The Claims
Claims 21-37 encompass a method for analysis of nucleic acid, the method comprising: obtaining a sample comprising (i) target nucleic acid comprising a locus and (ii) non- target nucleic acid comprising the locus, wherein the one of the (i) target nucleic acids and (ii) the non-target nucleic acid is methylated and the other is unmethylated; treating a sample with a methylation-specific restriction enzyme (MSRE) to selectively digest only the non-target nucleic acid; partitioning the sample into compartments; performing amplification in the compartments with detectably-labeled probes specific to the locus; and detecting any kind of signal from the probes to determine a quantity of the target nucleic acids that was present in the sample.
Working Examples
The specification provides no working example for determining a quantity of the target nucleic acids that is present in the sample by detecting any kind of signal from detectably-labeled probes using the methods recited in claims 21-37.
The Amount of Direction or Guidance Provided and The State of The Prior Art
The specification provides no working example for determining a quantity of the target nucleic acids that is present in the sample by detecting any kind of signal from detectably-labeled probes using the methods recited in claims 21-37. Furthermore, there is no experimental condition and/or experimental data in the specification to support the claimed invention. During the process of the prior art search, the examiner has not found any prior art which is related to determine a quantity of the target nucleic acids that is present in the sample by detecting any kind of signal from detectably-labeled probes using the methods recited in claims 21-37.
Level of Skill in The Art, The Unpredictability of The Art, and The Quantity of Experimentation Necessary
While the relative skill in the art is very high (the Ph.D. degree with laboratory experience), there is no predictability whether a quantity of the target nucleic acids that is present in the sample can be determined by detecting any kind of signal from detectably-labeled probes using the methods recited in claims 21-37.
Although the specification teaches that “[T]he amplified product in each droplet may be detected by, for example, a hydrolysis probe-based assay” and “[T]he invention is not limited to the TaqMan assay, as described above, but rather the invention encompasses the use of all fluorogenic DNA hybridization probes, such as molecular beacons, Solaris probes, scorpion probes, and any other probes that function by sequence specific recognition of target DNA by hybridization and result in increased fluorescence on amplification of the target sequence” (see paragraphs [0012] and [0095] of US 2024/0185950 A1, which is US publication of this instant case) and it is known that a TaqMan probe is an oligonucleotide probe consisting of a fluorophore covalently attached to the 5’-end of the oligonucleotide probe and a quencher at the 3’-end, before the TaqMan probe is used for a TaqMan assay, the quencher quenches the fluorescence emitted by the fluorophore and the TaqMan probe itself does not show a fluorescent signal produced from the fluorophore and during the TaqMan assay, degradation of the TaqMan probe releases the fluorophore from it and breaks the proximity to the quencher, thus relieving the quenching effect and allowing fluorescence of the fluorophore (see page 1 of “TaqMan” from Wikipedia), claim 21 does not indicate that detectably-labeled probes specific to the locus are what kind of probes. Since claim 21 does not require that amplifications in the compartments is a TaqMan assay and detectably-labeled probes are TaqMan probes which only produce a fluorescent signal during the TaqMan assay, if the detectably-labeled probes specific to the locus are probes labeled with a fluorescent dye which can produce a fluorescent signal before they hybridize to the locus of the target nucleic acid, without differentiating a fluorescent signal produced by the detectably-labeled probes themselves and a fluorescent signal produced in a process of amplification reactions, it is unpredictable how a quantity of the target nucleic acids that is present in the sample can be determined by detecting any kind of signal such as a fluorescent signal from detectably-labeled probes using the methods recited in claims 21-37. Furthermore, since claim 21 does not indicate that a signal from the detectably-labeled probes is what kind of signal and it is known that photomultiplier tubes (photomultipliers or PMTs for short) are extremely sensitive detectors of light in the ultraviolet, visible, and near-infrared ranges of the electromagnetic spectrum (see page 1 of “photomultiplier tubes” from Wikipedia), if the signal from the detectably-labeled probes is not a light signal, it is unpredictable how the signal can be detected using a detection apparatus comprising a photomultiplier tube as recited in claims 34-36.
Case law has established that “(t)o be enabling, 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’.” In re Wright 990 F.2d 1557, 1561. In re Fisher, 427 F.2d 833, 839, 166 USPQ 18, 24 (CCPA 1970) it was determined that “[T]he scope of the claims must bear a reasonable correlation to the scope of enablement provided by the specification to persons of ordinary skill in the art”. The amount of guidance needed to enable the invention is related to the amount of knowledge in the art as well as the predictability in the art. Furthermore, the Court in Genentech Inc. v Novo Nordisk 42 USPQ2d 1001 held that “[I]t is the specification, not the knowledge of one skilled in the art that must supply the novel aspects of the invention in order to constitute adequate enablement”.
In view of above discussions, the skilled artisan will have no way to predict the experimental results. Accordingly, it is concluded that undue experimentation is required to make the invention as it is claimed. The undue experimentation at least includes to test whether a quantity of the target nucleic acids that is present in the sample can be determined by detecting any kind of signal from detectably-labeled probes using the methods recited in claims 21-37.
Conclusion
In the instant case, as discussed above, the level of unpredictability in the art is high, the specification provides one with no guidance that leads one to claimed methods. One of skill in the art cannot readily anticipate the effect of a change within the subject matter to which the claimed invention pertains. Thus given the broad claims in an art whose nature is identified as unpredictable, the unpredictability of that art, the large quantity of research required to define these unpredictable variables, the lack of guidance provided in the specification, the absence of any working example related to claimed invention and the no teaching in the prior art balanced only against the high skill level in the art, it is the position of the examiner that it would require undue experimentation for one of skill in the art to perform the method of the claim as broadly written.
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.
Claims 21-37 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 21 is rejected as vague and indefinite in view of a methylation-specific restriction enzyme (MSRE). Since the specification does not have a definition for a methylation-specific restriction enzyme and the abbreviation “MSREs” in available arts means that methylation-sensitive restriction enzymes (see “Methylation-sensitive restriction enzymes (MSREs)”), it is unclear that a methylation-specific restriction enzyme (MSRE) in the claim means a methylation-sensitive restriction enzyme or not. Furthermore, if a methylation-specific restriction enzyme (MSRE) in the claim means a methylation-sensitive restriction enzyme which selectively digests only the non-target nucleic acid, the non-target nucleic acid must be unmethylated and the target nucleic acid must be methylated, the phrase “wherein the one of the (i) target nucleic acids and (ii) the non-target nucleic acid is methylated and the other is unmethylated” does not make sense.
Please clarify.
Claim 29 contains the trademark/trade names, VIC, FAM, and ROX. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe fluorophores, and, accordingly, the identification/description is indefinite.
Claim 30 recites the limitation “the first modification state” in the claim. There is insufficient antecedent basis for this limitation in the claim because there is no phrase “a first modification state” in claim 21. Furthermore, since claim 21 does not require that the sample is from a subject, it is unclear why a condition is needed to report to a subject. Please clarify.
Claim 37 is rejected as vague and indefinite because it is unclear which step in claim 21 is performed as a prenatal test for aneuploidy in a fetus. Please clarify.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 21-24, 27-29, and 37 are rejected under 35 U.S.C. 102 (a) (1) as being anticipated by Lo et al., (US 2009/0087847 A1, published on April 2, 2009).
Since it is known that a TaqMan probe is an oligonucleotide probe consisting of a fluorophore covalently attached to the 5’-end of the oligonucleotide probe and a quencher at the 3’-end, before the TaqMan probe is used for a TaqMan assay, the quencher quenches the
fluorescence emitted by the fluorophore and the TaqMan probe does not show a fluorescent signal from the fluorophore and during the TaqMan assay, degradation of the TaqMan probe releases the fluorophore from it and breaks the proximity to the quencher, thus relieving the quenching effect and allowing fluorescence of the fluorophore (see page 1 of “TaqMan” from Wikipedia), Lo et al., teach a method for analysis of nucleic acid, the method comprising: obtaining a sample (ie., maternal plasma taken from a pregnant woman carrying a trisomy 21 fetus) comprising (i) target nucleic acid comprising a locus (ie., HLCS gene in fetal DNA from the trisomy 21 fetus comprising hypermethylated locus) and (ii) non-target nucleic acid comprising the locus (ie., HLCS gene in maternal DNA from the pregnant woman carrying a trisomy 21 fetus comprising hypomethylated locus), wherein the one of the (i) target nucleic acids and (ii) the non-target nucleic acid is methylated and the other is unmethylated; treating a sample with a methylation-specific restriction enzyme (MSRE) (ie., HapII or BstUI) to selectively digest only the non-target nucleic acid; partitioning the digested sample (ie., putting diluted digested plasma DNA from the pregnant woman carrying a trisomy 21 fetus comprising hypomethylated HLCS gene) into compartments (ie., the reaction wells of a 384-well plate), performing amplification in the compartments with detectably-labeled probes specific to the locus (ie., TaqMan probes specific to HLCS gene); and detecting a signal (ie., a fluorescent signal from FAM) from the probes to determine a quantity of the target nucleic acid (eg., relative quantity of fetal HLCS gene by comparing total number of methylated HLCS counts from maternal plasma of the pregnant woman carrying a trisomy 21 fetus with total number of methylated HLCS counts from maternal plasma of a pregnant woman carrying a normal euploid fetus) that is present in the sample as recited in claim 21, the target nucleic acid comprises fetal nucleic acid and the sample comprises maternal blood or plasma as recited in claim 22, the non-target nucleic acid comprises maternal nucleic acid as recited in claim 23, measuring by digital PCR a quantity of a reference molecule (ie., RASSF1A gene in fetal DNA from the trisomy 21 fetus comprising hypermethylated locus) in the sample that is not digested by the MSRE; and quantifying the target nucleic acid by comparison to the measured reference molecule (ie., a ratio of HLCS gene to RASSF1A gene in fetal DNA from the trisomy 21 fetus) as recited in claim 24, scoring the sample for a fetal aneuploidy (ie., trisomy 21) as recited in claim 27, the detectably labeled probes comprise hydrolysis probes (ie., TaqMan probes) as recited in claim 28, each of the detectably labeled probes is labeled with a fluorophore selected from the group consisting of: VIC, FAM, an Atto dye, a cyanine dye, ROX, Cy5, Cy5.5, malachite green, and Texas red as recited in claim 29, and performing a prenatal test for aneuploidy in a fetus as recited in claim 37 (see paragraphs [0074] to [0079], [0252] to [0256], and [0305], and Figure 1).
Therefore, Lo et al., teach all limitations recited in claims 21-24, 27-29, and 37.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Frank Lu, Ph. D., whose telephone number is (571)272-0746. The examiner can normally be reached Monday to Friday, 9 AM to 5 PM.
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/FRANK W LU/
Primary Examiner, Art Unit 1683
September 17, 2026
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