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 .
DETAILED ACTION
Acknowledgement is hereby made of receipt and entry of the communication filed on Aug. 03, 2026. Claims 1-4, 6-20 are pending. Claims 8-20 are withdrawn. Claims 1-4, 6-7 are currently examined.
Claim Objection
(Previous objection- withdrawn) Claim 1 is objected for reciting a phrase “each subsample of only a subset of the subsamples including at least one of the viral particles” that need to be rewritten for clarification.
This objection is withdrawn in view of the amendment filed on 08/03/2026.
Claim Rejections - 35 USC § 112
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.
(Previous rejection-maintained with edition) Claims 1-4, 6-7 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.
The base claim 1 recites a phrase “the populations being defined based on the amplification data” that renders the claims indefinite. It is unclear what the criteria are needed to use the “the amplification data” to define a “population”. In addition, it is not clear if the “amplifying one or more targets from a genome of the viral particles and amplifying a first target from the template” generates the “amplification data” or not because the collected amplification data is from the subsamples as claimed.
Also, it is unclear how to amplify one or more targets from a gnome of the viral particles, and how to “amplifying a first target from the template”. Here, what is the relationship between the “viral particle”, “first target” or the “template”.
Claim 2 recites a phrase “…determining capsid occupancy by calculating a ratio using the counts or values derived from the counts” that render the claim indefinite. It is not clear what is meant by “counts” and “values”, and it is not clear how the “counts or values” can be derived from the “counts”. Also, it is unclear how the ratio is calculated and how its value is used to determine the capsid occupancy.
Claim 3 recites that phrase “comprise normalized subsample counts or subsample counts adjusted” that render the claim indefinite. It is unclear what the similarity and difference are between “subsample counts” or “subsample counts adjusted”. It is also not clear if the NPC is used only for the “subsample counts adjusted” or also it is needed for the “normalization”.
Claim 4 recites a phrase “the ratio includes the same tagging efficiency in both a numerator and a denominator such that the tagging efficiency cancels from the ratio” that renders the claim indefinite. It is unclear how the ratio is calculated, where the numerator and a denominator are from, which tagging efficiency is used to be compared to have “the same tagging efficiency” and what is meant by the phrase “the tagging efficiency cancels from the ratio”.
Claim 6 recites “…wherein tagging includes binding first and second proximity assay probes to the same capsid, the first and second proximity assay probes respectively” that render the claim indefinite. It is unclear if the tagging binds the capsid directly or binding the capsid through the probes, and how the tagging also includes binding the probes themself. It is also not clear how the “template” is created through a probe binding to the same capsid. Furthermore, it is unclear what the relationship is between the “a pair of oligonucleotides” and the “PA probes”, and how the pair of oligonucleotides are ligated and extended to create a template.
It is noted that generally, the claims as written are confusing and vague. Applicant is invited to rewrite the claims to be clearer and more concise.
Accordingly, one of ordinary skill in the art will not know the metes and bounds of the claims.
(Previous rejection- withdrawn) Claim 6 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential steps, such omission amounting to a gap between the steps. See MPEP § 2172.01.
This rejection is withdrawn in view of the amendment filed on 08/03/2026.
Claim Rejections - 35 USC § 112 (Written Description)
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.
(Previous rejection-maintained with edition) Claims 1-4 and 6-7 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the 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.
To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. See, e.g., Moba, B.V. v. Diamond Automation, Inc., 325 F.3d 1306, 1319, 66 USPQ2d 1429, 1438 (Fed. Cir. 2003); Vas-Cath, Inc. v. Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1116. However, a showing of possession alone does not cure the lack of a written description. Enzo Biochem, Inc. v. Gen-Probe, Inc., 323 F.3d 956, 969-70, 63 USPQ2d 1609, 1617 (Fed. Cir. 2002). For example, it is now well accepted that a satisfactory description may be found in originally-filed claims or any other portion of the originally-filed specification. See In re Koller, 613 F.2d 819, 204 USPQ 702 (CCPA 1980); In re Gardner, 475 F.2d 1389, 177 USPQ 396 (CCPA 1973); In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976). However, that does not mean that all originally-filed claims have adequate written support. The specification must still be examined to assess whether an originally-filed claim has adequate support in the written disclosure and/or the drawings. See MPEP 2163. I.
In Regents of the University of California v. Eli Lilly and Co. 119 F.3d 1559, 43 USPQ2d 1398 (Fed. Cir. 1997), the Court decided that adequate written description of genetic material "requires a precise definition, such as by structure, formula, chemical name, or physical properties, not a mere wish or plan for obtaining the claimed chemical invention." Id. 43 USPQ2d at 1404 (quoting Fiefs, 984 F.2d at 1171, 25 USPQ2d at 1606). In AbbVie Deutschland GMBH & Co. v. Janssen Biotech, Inc. (Court of Appeals, Federal Circuit 2014), the Court ruled that “[W]ith the written description of a genus, however, merely drawing a fence around a perceived genus is not a description of the genus. One needs to show that one has truly invented the genus, i.e., that one has conceived and described sufficient representative species encompassing the breadth of the genus. Otherwise, one has only a research plan, leaving it to others to explore the unknown contours of the claimed genus. See Ariad, 598 F.3d at 1353 (The written description requirement guards against claims that “merely recite a description of the problem to be solved while claiming all solutions to it and . . .cover any compound later actually invented and determined to fall within the claim' s functional boundaries.”).”
The amended base claim 1 is directed to a method of analyzing viral particles, the method comprising: tagging capsids of the viral particles with a tag wherein the tag includes a template forming subsamples of a sample containing the viral particles, wherein only a subset of the subsamples contains at least one of the viral particles; amplifying one or more targets from a genome of the viral particles, and amplifying a first target from the template; collecting amplification data from the subsamples, wherein the data includes amplification for the first target, and amplification data for the one or more targets from the genome; and enumerating populations of the subsamples, the populations being defined based on
Based on the instant base claim 1, the tagging capsids of the viral particles with a tag can form subsample. However, the instant specification discloses that the tagging capsids of the viral particles with a tag can form partitions not subsample (See instant specification, Fig. 2 and below). The instant specification discloses that the “"Partitions" are discrete volumes of fluid (i.e., fluid volumes) that are isolated from one another (also called isolated volumes). Each partition of a set of partitions may contain a portion of the same sample. The partitions may be separated from one another by fluid (e.g., oil or air), a wall(s) of a device(s), or a combination thereof, among others. Accordingly, the partitions may be droplets of an emulsion, or volumes held by wells, chambers (e.g., nanochambers having a capacity ofless than 1 μL), tubes (e.g., micro tubes having a diameter of less than 1 mm), or microfluidic devices, among others. The partitions may be the same diameter as one another and/or may be composed of the same amount of fluid as one another” (See Instant specification, [0056]). Here the descriptions define the meaning of the “partitions “ but does not provide evidence to support if the “partitions” and “subsample” are the same or not. Thus, there is no evidence to support or demonstrate that the tagging capsids of the viral particles with a tag, wherein the tag includes a template, can form subsamples as claimed.
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Claim 2 states enumerating includes obtaining subsample counts for two or more of the populations and determining capsid occupancy by calculating a ratio using the counts or values derived from the counts. However, the instant specification discloses that the “enumeration value" is any value that results from enumerating a tag/target-defined subset of a set of subsamples/partitions in a digital assay (See [0041]) and the quantification of capsid occupancy using partition population counts (See [0113]), and linkage concentrations (See [0125]). It does not describe how the counts are related to the digital assay and concentrations. Thus, the specification has failed to sufficiently describe how the enumerating is obtained and how the capsid occupancy can be determined.
At the same time, the instant specification does not clarify where the “counts” are from and how to normalize and adjust the counts with NPC in claim 3. For example, the instant specification discloses that the NPC background signal needs to be corrected (See [0121]), however, it does not describe how the NPC background needs to be corrected in order to adjust each count. Also, the instant specification does not disclose how the tagging efficiency cancels from the ratio as claimed in claim 4. For claim 6, the Fig. 17 of the instant specification discloses that multiple copies of tagging probe 444 can bind to the same capsid 436, to increase the signal detectable from label 490 for a given labeled viral particle 434 (See [0147]), but does not discloses how to perform “the first and second proximity assay probes respectively” as claimed, and does not clarify if the tagging probe, the first and second oligonucleotides or both to be involved in the assay.
In addition, the instant base claim 1 only recites one amplification step at “amplifying one or more targets from a genome of the viral particles”. However, the instant specification discloses a flow diagram schematically illustrating two amplification steps (See Fig. 3 and below). In [0107] of the instant specification, it discloses that the amplification reagents include a pair of first primers 168a, 168b to amplify a first target 170 from template 164, and a first amplification probe 171 for detecting amplification of first target 170 (see FIG. 5 and below). The amplification reagents also include a pair of second primers 172a, 172b for amplification of a second target 174 from genome 138, and a second amplification probe 175 for detecting amplification of second target 174 (see FIG. 6 and below).
Accordingly, there is no evidence to support or demonstrate in the instant specification that the amplification is only for the targets from a genome of the viral particles as claimed.
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Accordingly, the full breadth of the claims does not meet the written description provision of 35 U.S.C. 112, first paragraph. The specification does not provide sufficient written description support for the invention as claimed.
Responses to Applicant’s Remarks
Applicant’s arguments filed on 08/03/2026 has been received and fully considered.
Applicant’s amendment regarding the objection is considered. The objection is withdrawn.
Applicant’s argument regarding rejections under 35 U.S.C. § 112(a) and§ 112(b) are not found persuasive. The amended claims regarding amplifiable nucleic acid template, tag on a capsid, proximity ligation assay and determine viral occupancy are still vague and not clear. See the rejections above.
Therefore, the rejections are maintained with editions based on the amendment.
Conclusion
No claims are allowed.
Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RUIXUE WANG whose telephone number is (571)272-7960. The examiner can normally be reached Monday-Friday 8:00 am-5:00 pm, EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Thomas J. Visone can be reached on (571) 270-0684. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/RUIXUE WANG/ Examiner, Art Unit 1672
/NICOLE KINSEY WHITE/Primary Examiner, Art Unit 1672
