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 . Applicant’s amendment filed 1/30/2026 is acknowledged. Claims 1 and 10 have been amended. Claims 7-8 have been canceled. Claims 1-6, 9 and 10 are pending. All of the amendment and arguments have been thoroughly reviewed and considered.
Any rejection not reiterated in this action has been withdrawn as being obviated by the amendment of the claims.
This action is made Final.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Previous Rejections
The objection to the specification was withdrawn in view of Applicant’s amendment of the specification. The claim rejections under 35 USC 112(b) directed to the claims 1-10 is withdrawn in view of Applicant’s amendment of the claims. The prior art rejection under 35 USC 103 directed to the claim 10 as being unpatentable over Alcaide et al in view of Ahern is withdrawn in view of the new ground(s) of rejection necessitated by applicant’s amendment of the claims. The prior art rejection under 35 USC 103 directed to the claim 10 as being unpatentable over Deakin et al in view of Ahern is withdrawn in view of the new ground(s) of rejections necessitated by applicant’s amendment of the claims.
New Ground(s) of Rejections
THE NEW GROUND(S) OF REJECTIONS WERE NECESSITATED BY APPLICANT’S AMENDMENT OF THE CLAIM:
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-6 and 9 are rejected under 35 U.S.C. 101 because the claimed invention is directed to without significantly more.
35 U.S.C. 101 reads as follows:
According to the 2019 Revised Patent Subject Matter Eligibility Guidance, an initial two step analysis is required for determining statutory eligibility.
According to the Manual of Patent Examination Procedure (MPEP) sections 2103 through 2106.07(c), which now incorporates the 2019 Revised Patent Subject Matter Eligibility Guidance (2019 PEG), October 2019 Patent Eligibility Guidance Update (October 2019 Update), and the Berkheimer Memo, an initial two step analysis is required for determining statutory eligibility.
Step 1 requires a determination of whether the claims are directed to a process, machine, manufacture, or a composition of matter. In the instant case, the Step 1 requirement is satisfied as the claims are directed towards a process.
Step 2
The Step 2 analysis is a two-part analysis, Step 2A and Step 2B.
Step 2A. prong 1
Step 2A, prong 1 requires a determination of whether the claims are directed towards a judicial exception, i.e. a law of nature, natural phenomenon, or an abstract idea, while step 2A, prong 2 requires an analysis of whether the judicial exception integrated into a practical application if the claim recites a judicial exception under Prong 1.
The claims recited the judicial exception of an abstract idea. The claims 1-6 and 9 are directed towards a judicial exception, abstract ideas of generating a cluster by grouping information, obtaining sequence information, selecting UID and linking UID information to form initial cluster and expanded cluster information using general computer programs, software programs or mental analyses such as reading information on a computer screen or in the mind.
The claims recite a method for generating a consensus sequence for detecting a target nucleic acid, the method comprises amplifying DNA fragments from a sample using polymerase chain reaction (PCR) with primer containing adapter sequences, flanking sequences, and UID sequences, in the direction from the 5’ end to the 3’ end, obtaining sequence information of the amplified DNA fragments through the PCR and generating a cluster by grouping a plurality of the amplified DNA fragments derived from a single starting DNA molecule based on the sequence information using a peer-to-peer (P2P) network method, wherein the generating a cluster comprises:
(a) obtaining, from the sequence information, sequence information of a UID pair comprising a first UID and a second UID located at opposite ends of the ach of the amplified DNA fragments; (b) selecting one UID as a seed UID and linking all UIDSs paired with the seed UID to form an initial cluster; and (c) recursively linking other UIDs that are paired with UIDs included in the initial cluster to expand the cluster (claim 1).
The claims 2-6 and 9 embodies the limitation of the claim 1.
In the instant case, the claims are drawn to the method(s) recited above comprising steps of utilizing computer processor/computer programs and/or software programs to generate cluster and cluster information. The result of Step 2A analysis is that the claims are directed towards a judicial exception, i.e., abstract idea specifically in the steps of generating cluster comprising the steps (a)-(c). The steps recite the use of a computer, computer program or software and mathematical calculations/algorithms to obtain sequence information and generating cluster information using peer-to-peer (P2P) network method (claim 1) and a step of trimming the sequence information (step 3).
The Court has made clear if a claim is directed essentially to a method of calculating, using a mathematical formula, even if the solution is for a specific purpose, the claimed method is non-statutory. In other words, patenting abstract ideas cannot be circumvented by attempting to limit the use [the idea] to a particular technological environment. In the instant case, the steps of generating a clyster information and steps recited to be involved in peer-to-peer network method and product amounting therefrom are considered mere instructions to implement an abstract idea. The recitation of a peer-to-peer network method recited by the method claims do not offer a meaningful limitation beyond generally linking “the use of the method to a particular technological environment,’ that is, implementation via computers/software programs and/or mathematical calculations.” see Alice Corp v. CLS Bank Int’l 573 U.S. (2014). According to Recent Subject matter eligibility discussion McRO, Inc. dba Planet Blue v. Bandai Namco Games America Inc., 120 USPTQ2d 1091 (Fed. Cir. 2016), "An "improvement in computer related technology” is not limited to improvements in the operation of a computer or a computer network per se, but may also be claimed as a set of “rules” (basically mathematical relationship) that improve computer-related technology by allowing computer performance of a function not previously performable by a computer”. The limitation recites steps of manipulating and/or gathering data using computer-implemented program steps/calculations or software programs such as a peer-peer (P2P) network method comprising the steps recited in the claim 1. These steps do not provide a physical contribution to the computer function or structure and could be performed using any general computer and/or mental steps of reading information on a screen.
Step 2B
The second part, Step 2B of the two-step analysis is drawn to determining whether any element or combination of elements, in the instant claims is/are sufficient to ensure that the claims as a whole amount to significantly more than the judicial exception. In this case, the steps of amplifying DNA fragments from a sample using PCR with primer containing adapter sequence, flanking sequence and UID sequences in the directions from the 5’ end to the 3’ end and obtaining sequence information of the amplified DNA through the PCR comprises of well-understood and routine and conventional activity already engaged in by the scientific community as evidence by Alcaide et al (Scientific Reports, September 2017, citation made of record on IDS herein) teach a PCR method and a PCR primer comprising adapter sequences, a flanking sequence and a UID sequence used in the amplification method to generate sequence information (see method section and Figure 1 and Legend, and section entitled “Library Preparation”, first paragraph at page 2.4) and Deakin et al (Nucleic Acids Research, vol. 42, no. 16, e129, 1-14, July 2014) which teach a PCR primer comprising adapter sequences, a flanking sequence and a UID sequence (The reference teaches a partial Illumina adaptor which comprise a primer sequence, a barcode sequence and flanking sequence near the barcode sequence Figure 1 and legend). The additional limitations, which have been found to be known and routine in the art, do not transform the abstract idea into a patent eligible application of the abstract idea such that the claims amount to significantly more than the abstract idea. Likewise, the clams 2-6 and 9 are recited at a high level of generality such that they do not recited any significant information which transforms the patent ineligible subject matter into eligible subject.
The Court has made clear that to transform an unpatentable law of nature into patent-eligible application of such a law, one must do more than simply state the law of nature while adding the words “apply it”. Essentially, appending conventional steps or elements, specified at a high level of generality, to laws of nature, natural phenomena, and abstract ideas cannot make those laws, phenomena, and ideas patent-eligible. The Supreme Court also indicated that any additional steps that simply are routine and conventional in the art are insufficient to transform an otherwise patent-ineligible process.
In view of the foregoing, the claims are not drawn to patent eligible subject matter under 35 USC 101.
Claim Rejections - 35 USC § 103
The following are new grounds of rejections necessitated by Applicant's amendments. Although the claims were previously rejected as being anticipated and/or unpatentable over the same reference(s), Applicant's amendments have necessitated the inclusion of new grounds of rejections in this Office action. It is noted that, to the extent that they apply to the present rejection; Applicant's arguments are addressed following the rejection.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim(s) 10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Alcaide et al (Scientific Reports, September 2017, citation made of record on IDS herein) in view of Ahern (The Scientist, https://www.the-scientist.com/technology/biochemical-reagents-kits-offer-scientists-good-return-on-investment-58425, pages 1-5, July 1995).
Claim 10 is directed to a kit for performing the method for generating a consensus sequence for target nucleic acid detection of claim 1 comprising a PCR primer comprising an adapter sequence, a flanking sequence and a UID sequence in a direction from a 5’ end to a 3’ end. It is noted that the limitation “for performing the method for generating a consensus sequence for target nucleic acid detection of claim 1” is a recitation of the intended. MPEP states that “intended use for a product describes what the invention is intended to do rather than its structure. According to MPEP, the intended use does not carry the same weight as functional limitations, which may be given patentably weight if they impose structural or operational distinctions (See MPEP 2114). MPEP further states that if the prior art structure is capable of performing the intended use, then it meets the claims.
With regards to claim 10, Alcaide et al teach a PCR primer comprising adapter sequences, a flanking sequence and a UID sequence (see Figure 1 and section entitled “Library Preparation”, first paragraph at page 2.4). Alcaide does not teach wherein the structure is in the form of a kit.
Ahern provides a general teaching of the advantages of providing reagents in the form of a kit. Ahern teaches that a kit offers scientists the opportunity to better manage their time, putting these products all together in kits take the convenience one step further. Ahern teaches that the amount of time that researchers save makes purchasing products in a kit is cost effective and save the practitioner time (see page 3, paragraphs 5 and 7). Thus, it would have been prima facie obvious to one of ordinary skill in the art at the time of the effective filing date of the claims invention to provide the primer structure as taught by Alcaide et al for the ease and convenience of use to the practitioner in a cost-efficient manner as suggested by Ahern.
8. Claim(s) 10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Deakin et al (Nucleic Acids Research, vol. 42, no. 16, e129, 1-14, July 2014) in view of Ahern (The Scientist, https://www.the-scientist.com/technology/biochemical-reagents-kits-offer-scientists-good-return-on-investment-58425, pages 1-5, July 1995).
Regarding claim 10, Deakin et al teach a PCR primer comprising adapter sequences, a flanking sequence and a UID sequence (The reference teaches a partial Illumina adaptor which comprise a primer sequence, a barcode sequence and flanking sequence near the barcode sequence Figure 1 and legend). Deakin does not teach wherein the structure is in the form of a kit.
Ahern provides a general teaching of the advantages of providing reagents in the form of a kit. Ahern teaches that a kit offers scientists the opportunity to better manage their time, putting these products all together in kits take the convenience one step further. Ahern teaches that the amount of time that researchers save makes purchasing products in a kit is cost effective and save the practitioner time (see page 3, paragraphs 5 and 7). Thus, it would have been prima facie obvious to one of ordinary skill in the art at the time of the effective filing date of the claims invention to provide the primer structure as taught by Deakin et al for the ease and convenience of use to the practitioner in a cost-efficient manner as suggested by Ahern.
Response to Arguments
9. Applicant traverses the rejection on the following grounds:
Applicant’s Traversal over Alcaide et al
(a) Applicant summarizes the Examiner’s rejections and states that Alcaide teaches a fundamentally different, ligation-based method and summarizes the teachings of Acaide et al. Applicant states that in contrast to the present invention which utilizes a UID-containing PCR primer. Applicant states that the UID is introduced into the daughter strands during the PCR amplification process itself, completely obviating the need for a separate, inefficient ligation step. Applicant states that it represents a fundamentally different technical approach. Applicant states that Applicant’s specification at pages 6 and 7, this distinction enables a significant and unexpected advantage namely the ability to perform a higher number of PCR cycles for UID incorporation, wherein ligation - based methods are limited. Applicant states that therefore, the primer of the present invention is structurally and functionally distinct from the components used in Alcaide’s method and one of ordinary skill in the art would not have considered them to be interchangeable.
Applicant’s traversal over Deakin
(b) Applicant states while Deakin discusses using barcodes to reduce sequencing errors, its method is limited to the conventional approach of simply grouping reads that share an identical barcode to form consensus. Applicant states that Deakin provides no teaching or suggesting of the Applicant’s core inventive concept using UID pairs to reconstruct the entire amplification lineage of a single starting molecule through a P2P network algorithm. Applicant states that the sophisticated, network-based lineage reconstruction is entirely absent from the simple grouping method of Deakin. Applicant states based on the claim as amended, the rejection should be withdrawn.
Examiner’s response
10. All of the amendment and arguments have been thoroughly reviewed and considered but are not found persuasive for the reasons that follow:
i) In response to applicant’s arguments above at a) and b), the examiner acknowledges Applicant’s arguments but respectfully disagrees. Applicant is once again reminded that the claims are directed to a product and not a method. It is noted that the limitation “for performing the method for generating a consensus sequence for target nucleic acid detection of claim 1” is a recitation of the intended of the claimed primer. No specific limiting structure is recited besides the components recited in the claim 10. MPEP states that “intended use for a product describes what the invention is intended to do rather than its structure. According to MPEP, the intended use does not carry the same weight as functional limitations, which may be given patentably weight if they impose structural or operational distinctions (See MPEP 2114). MPEP further states that if the prior art structure is capable of performing the intended use, then it meets the claims. In this case the functional limitation applicant makes reference to is it’s use in the method of claim 1 (intended use). In the method of claim 1, the primer is used for amplification in a PCR reaction which is the same use of the primer(s) of the cited prior art of Alcaide and Deakin. However, in the case of the claim 10, the claimed primer is defined by “what is” (e.g., primer comprising of component parts or structural parts) and not how it intends to function in a method, such as the method of invention 1. MPEP states that typically no patentable distinction is made by an intended use or results unless some structural difference is imposed by the use. In this case no structural difference is imposed by the intended use of the primer in an amplification-based reaction. Accordingly, the examiner maintains that the teachings of Alcaida and Deakin meets the limitations of the claims and accordingly, the claim 10 is rejected under 35 USC 103.
Conclusion
11. No claims are allowed. Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. 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 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.
12. Any inquiry concerning this communication or earlier communications from the examiner should be directed to CYNTHIA B WILDER whose telephone number is (571)272-0791. The examiner can normally be reached Flexible.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, GARY BENZION can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/CYNTHIA B WILDER/Primary Examiner, Art Unit 1681