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 .
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 10/22/2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Objection to Specification
The disclosure is objected to because of the following informalities:
The use of the following trade names or marks in the specification, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
At page 4, line 2, "TaqMan" (serial # 78289347, owned by Roche Molecular Systems, Inc.);
At page 3, line 26, "QX200" (serial #90775541, owned by Bio-Rad Laboratories, Inc.);
At page 3, lines 22, 27; page 4, lines 23-24; page 5, line 4; page 7, lines 21-22 "ddPCR" (serial # 77944227, owned by Bio-Rad Laboratories, Inc.);
At page 4, line 2; page 5, lines 2-3; page 7, line 29; page 8, lines 3-6, 14, 26, "FAM" (trademark of Applera Corporation, Inc.1);
At page 4, line 2; page 5, lines 2-3; page 7, line 29; page 8, lines 3-6, 14, 26, "HEX" (trademark of Applera Corporation, Inc.);
At page 4, line 2; "VIC" (trademark of Applera Corporation, Inc.).
Regarding the terms above, trademark symbols are not used to denote the tradenames and should be added. Further, each letter in the trademark should be capitalized.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Status of Claims
This office action is in response to Applicant's Response to Election / Restriction filed on August 28, 2026.
Claims 1-8 are pending, with claim 7 withdrawn.
Claims 1-6 and 8 are under examination. This is the first action on the merits.
Election/Restrictions
Applicant’s election without traverse of the following species in the reply filed on August 28, 2026 is acknowledged:
Species of Target Analyte: B) the target analytes are genomic DNA ;
Species of sub-fragments: D) the sub-fragments are on the same fragment but separated by an intervening sequence (claim 8)2.
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)).
Claim 7 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention.
Examination on the merits commences on claims 1-6 and 8.
Priority
The priority date of the instant claims 1-6 and 8 is 05/19/2023, filling date of the US provisional application NO. 63/503,365.
Claim Objections
Claims 3-4 are objected to because of the following informalities:
In claim 3, line 2, "the droplet" should read "the droplets," to properly reference "a plurality of droplets" recited in base claim 1.
Accordingly, claim 4 which depends from claim 3 should read:
"The method of claim 3, wherein the droplets are s surrounded by an immiscible fluid.”
Claim Rejections - 35 USC § 112(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.
Claims 1-6 and 8 are rejected under 35 U.S.C. 112(b), 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.
A) Claim 1 recites:
A method for quantifying linked molecules, the method comprising the steps of:
preparing a plurality of droplets, each comprising nucleic acid fragments obtained from a biological sample;
selecting a species of N linked nucleic acid fragments for detection, wherein N is the number of different sub-fragments that comprise the linked species;
assaying the droplets to determine a subset of linked species that contain fewer than N linked sub-fragments, and a subset of each of the sub-fragments alone; and
quantifying the N linked nucleic acid fragments as the average of a total for each sub-fragment less a total of linked species less than N comprising the sub-fragment.
However, several aspects of the claim renders its scope indefinite.
A1- It is unclear what "N" refers to in the recitation "a species of N linked nucleic acid fragments."
The claim recites "selecting a species of N linked nucleic acid fragments for detection, wherein N is the number of different sub-fragments that comprise the linked species."
However, it is unclear:
whether "N" refers to the number of copies of a nucleic acid in the sample that comprise a particular linked species, such as 1000 copies of a BCR-ABL1 fusion fragment; or
whether "N" refers to the number of different types of nucleic acid sequences that make up the linked species, such as two sequence portions in a BCR-ABL1 fusion fragment.
The specification appears to suggest that N refers to the number of different types of nucleic acid sequences that make up the linked species. For example, the specification describes a "three-target linked species (ABC)" and "fewer than three target-linked species" comprising AB, BC, AC, A, B, C.
"For example, if copies per droplet of a three-target linked species (ABC) is to be quantified, then clusters of droplets positive for the ABC three target linked species are selected. Then, clusters of droplets positive for fewer than three target-linked species are selected. For example, droplets positive for AB, BC, AC, A, B, C are also selected." (page 2, lines 24-27)
However, this example does not resolve the indefiniteness in the claim language because it appears to conflict with the claim. The claim recites that "N is the number of different sub-fragments that comprise the linked species," which requires the sub-fragments to comprise the linked species. However, in the specification's example, AB, BC, AC, A, B, C do not comprise ABC.
A2-The metes and bounds of "species of N linked nucleic acid fragments," "sub-fragments," and "a subset of linked species" are unclear.
It is unclear what is encompassed by the claimed "species of N linked nucleic acid fragments." The application's disclosure does not provide a clear definition of this term. The claim further recite "wherein N is the number of different sub-fragments that comprise the linked species." However, in view of the example in the specification discussed above, it is unclear whether the claimed "species of N linked nucleic acid fragments" is required to encompass A, B, C only; or whether it is also required to encompass AB, BC, AC, in order to be considered as being comprised by the different sub-fragments, as required by the claim.
The next step recites assaying "a subset of linked species." It is unclear whether this refers to a subset of the previously recited "species of N linked nucleic acid fragments," or to some other linked species.
A3- The scope of the quantifying step is unclear.
It is unclear how the quantifying step is required to be performed. The claim recites "quantifying the N linked nucleic acid fragments as the average of a total for each sub-fragment less a total of linked species less than N comprising the sub-fragment." This limitation is indefinite because it is both grammatically unclear and mathematically unclear.
First, the phrase "less a total of linked species less than N comprising the sub-fragment" is grammatically unclear. It is unclear what noun is modified by "less than N," and it is unclear how the phrase "comprising the sub-fragment" relates to the rest of the limitation.
Second, the limitation is also mathematically unclear. The step appears to require a calculation, but it does not clearly state what values are required as inputs or how the calculation mush be carried out. The claim does not clearly identify what values are being added, subtracted, or averaged. For instance, the phrase "a total for each sub-fragment" does not identify whether the "total" refers to a count of droplets, a count of detected nucleic acid sub-fragments (e.g., a count of A, B, or C), a count of linked species (e.g., a count of AB, BC, AC, or ABC), or some other value.
The phrase "less a total of linked species less than N comprising the sub-fragment" also does not clearly identify what value is being subtracted or compared, thus making it unclear what mathematical operation the claim requires. In particular, "less than" ordinarily denotes comparison rather than subtraction; while "less" may suggest subtraction. As currently written, the phrase does not clearly identify what value, if any, is being subtracted, what value is being compared, and how "less than N" modifies the surrounding language. Accordingly, the claim does not clearly convey the scope of the quantifying limitation. Applicant is advised to clarify this limitation by reciting an objective formula, equation, or set of calculation steps in a clear and unambiguous manner.
In conclusion, the cumulative ambiguity in the claim, as discussed above, renders claim 1 indefinite. Claims 2-6 and 8 are rejected for depending from claim 1 and not remedying the indefiniteness.
The numerous instances of indefiniteness issues in claim 1 and its dependent claims are compounding, making it impossible for a person of ordinary skill in the art to determine the metes and bounds of the claimed invention without relying on extensive speculation and assumptions. Consequently, claims 1-6 and 8 are excluded from prior art search in this examination, as any rejection based on prior art cannot be based on speculations and assumptions, see In re Steele, 305 F.2d 859, 862 (CCPA 1962).
For compact prosecution, applicant is advised to amend the claims to clarify the metes and bounds of the claims, so the claims can be examined.
Key issues that must be resolved to determine the scope of the claim include:
The metes and bounds of the terms "species of N linked nucleic acid fragments," "sub-fragments," and "a subset of linked species" need to be clearly identified.
What is the relationship between these terms and what components are required to comprise the others?
Clarify which nucleic acid fragments and/or species are being assayed and quantified.
B) Claim 5 recites "the digital polymerase chain reaction," which lacks antecedent basis.
The base claim 1 does not recite a "digital polymerase chain reaction."
The term "digital polymerase chain reaction" is introduced in claim 2, but claim 5 does not depend therefrom.
C) Claim 6 recites "wherein N is from about 3 to about 10," which is indefinite for its recitation of "about," without defining the term in the specification. The term "about" is unclear because it is subjective and fails to provide clear boundaries for the claim's scope.
The lack of definition of "about" makes the scope of the claim unclear because the term introduces ambiguity in the meets and bounds of the claimed value. It is unclear to what extent a value may vary to still be considered "about" a specific number. For instance, it is unclear whether values such as 2, 2.5, or 12 are encompassed by the claimed range "about 3 to about 10."
Prior Art
Although no prior art is applied to the claims in this Office Action due to indefiniteness issues discussed above, the prior art references below are made of record by the examiner as references of interest.
The following references teach methods for assessing linked nucleic acid molecules using droplet digital PCR:
Barron (Barron et al., Quantification of the mobility potential of antibiotic resistance genes through multiplexed ddPCR linkage analysis, FEMS Microbiology Ecology, Volume 99, Issue 4, April 2023, fiad031,; doi.org/10.1093/femsec/fiad031), see Figure 1;
Zanker (Zanker et al., Insight and Development of Advanced Recombinant Adeno-Associated Virus Analysis Tools Exploiting Single-Particle Quantification by Multidimensional Droplet Digital PCR. Hum Gene Ther. 2022 Sep;33(17-18):977-989. doi: 10.1089/hum.2021.182. Epub 2022 Apr 28. PMID: 34937401; PMCID: PMC10112877); see Figure 3;
Regan (Regan et al., A rapid molecular approach for chromosomal phasing. PLoS One. 2015 Mar 4;10(3):e0118270. doi: 10.1371/journal.pone.0118270. PMID: 25739099; PMCID: PMC4349636));
Regan2 (Regan et al., (2018). Phasing DNA Markers Using Digital PCR. In: Karlin-Neumann, G., Bizouarn, F. (eds) Digital PCR. Methods in Molecular Biology, vol 1768. Humana Press, New York, NY.; doi.org/10.1007/978-1-4939-7778-9_28);
US20120322058A1- Analysis of nucleic acids, see claim 61;
US20160362729A1- Methods and compositions for chromosome mapping; see FIG. 31;
US20130059754A1- Digital assays with reduced measurement uncertainty; see [0028];
US20150038356A1 - Genetic assays; see example 1;
US20140274786A1- Digital assays with associated targets;
US20160076099A1 - Analysis of nucleic acids.
Conclusion
Claims 3-4 are objected to; Claims 1-6 and 8 are rejected. No claims are allowed.
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/TIAN NMN YU/Examiner , Art Unit 1681
1 See Bio-Rad( MiniOpticon™ System; 2012), page 2 : "FAM, HEX, VIC, and ROX are trademarks of Applera Corporation."
2 Claim 7 is withdrawn as being drawn to non-elected species C
