DETAILED ACTION
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 examiner 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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office Action has been withdrawn pursuant to 37 CFR 1.114.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 05/19/2025 has been entered.
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 .
Claims Status
Claims 2, 3, 10, and 11 are canceled.
Claims 30-33 are new.
Claims 1, 5-9, 12, and 21-33 are pending.
Claims1, 5-9, 12, and 21-33 are examined.
Information Disclosure Statement
The Information Disclosure Statements filed 05/19/2025, and 09/08/2025 are in compliance with the provisions of 37 CFR 1.97 and have therefore been considered. Signed copies of the IDS documents are included with this Office Action.
Withdrawn Rejections/Objections
The rejection of claim 21 under 35 USC 112(d) is withdrawn in view of the amendments submitted.
The rejection of claims 1-3, 5-13, and 21-29 under 35 USC 103 as being unpatentable over Bonyhadi et al. (US 2019/0345543 A1) in view of Diggans (US 2017/0357752 A1) is withdrawn as Bonyhadi et al. is not directed to identifying genetic engineering in a query sequence.
Rejections and/or objections not reiterated from previous office actions are hereby withdrawn in view of the amendments filed 12/9/2010. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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, 5-9, 12, 21-29, and 31-33 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to an abstract idea of mental steps, mathematic concepts, or a natural law without significantly more. Any newly recited portion is necessitated by claim amendment.
Claim 30 is eligible under 35 USC 101 because the limitation of “preventing a release of the biological specimen in response to the identification of the presence of genetic engineering in the biological specimen” integrates the judicial exceptions into a practical application.
The MPEP at MPEP 2106.03 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of
matter?
(2A)(1) Are the claims directed to a judicially recognized exception, i.e. a law of nature,
a natural phenomenon, or an abstract idea?
(2A)(2) If the claims are directed to a judicial exception under Prong One, then is the
judicial exception integrated into a practical application?
(2B) If the claims are directed to a judicial exception and do not integrate the judicial
exception, do the claims provide an inventive concept?
With respect to step (1): Yes, the claims recite a method and a computing device.
With respect to step (2A)(1): The claims recite an abstract idea of mental processes, and recites laws of nature.
“Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection” (MPEP 2106.04). Abstract ideas include mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (procedures for observing, evaluating, analyzing/judging and organizing information (MPEP 2106.04(a)(2)). Laws of nature or natural phenomena include naturally occurring principles/relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature (MPEP 2106(b)).
Mental processes recited in claims 1 and 9:
determining one or more regions of interest in the query sequence, wherein each region of interest comprises part of a whole protein translated region
determining whether a match for a genetic engineering context signature exists in the query sequence adjacent to any of the one or more regions of interest of the query sequence, wherein the genetic engineering context signature comprises a sequence selected from a database of sequences indicative of genetic engineering, and wherein determining whether the match for the genetic engineering context signature exists adjacent to any of the one or more regions of interest comprises searching upstream or downstream of each region of interest over a predetermined search range that is particular to a context signature type of the sequence selected
Dependent claims --5-8, 12, 21-23, 25, 26, 28, 29 and 31-33 recite additional steps that either are directed to abstract ideas or further limit the abstract ideas in independent claims 1 and 9 and as such, are further directed to abstract ideas. Hence, the claims explicitly recite numerous elements that individually and combination constitute abstract ideas. The relevant recitations are:
Claims 5 and 12: “genetic engineering context signature comprises an upstream regulatory element, a downstream regulatory element, or a tag”
Claims 6 and 22: “genetic engineering context signature comprises an upstream regulatory element, wherein the upstream regulatory element comprises a promoter, a ribosome binding site, an operator that contributes to transcript regulation, or an enhancer”
Claims 7 and 23: “genetic engineering context signature comprises a downstream regulatory element, wherein the downstream regulatory element comprises a terminator, a polyA site, a woodchuck hepatitis virus posttranscriptional regulatory element (WPRE), a C-terminal expansion (CTE), or long terminal repeat (LTR)” Claims 8 and 21: “genetic engineering context signature comprises a tag, wherein the tag comprises a purification/epitope tag, a cleavage sequence, or a targeting sequence”
Claims 25 and 28: “the sequence of the genetic engineering context signature regulates transcription of an associated region of interest of the query sequence”
Claims 26 and 29: “a start of the predetermined search range is no more than 800 base pairs upstream of each region of interest and an end of the predetermined search range is no more than 1200 base pairs downstream of each region of interest”
Claims 31 and 33: “the identification of the presence of genetic engineering in the biological specimen is configured to assist in determining culpability for a release of the biological specimen”
Claim 32: “the identification of the presence of genetic engineering in the biological specimen is configured to prevent a release of the biological specimen”
The abstract ideas recited in the claims are evaluated under Broadest Reasonable Interpretation (BRI) and determined herein to each cover mental processes because the claims comprise no more than performing mental processes to determine that there is a match for a genetic engineering context sequence.
Because the claims do recite judicial exceptions, direction under (2A)(2) provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application (MPEP 2106.04(d). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d).I; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim is said to fail to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
With respect to the instant recitations, claims 1 and 9 recite the following additional elements:
Claim 1
receiving a query sequence obtained for the biological specimen
transmitting an identification of the presence of genetic engineering in the biological specimen in response to determining that the match exists
a computing device to perform the method
Claim 9
computing device comprising a query mapper and a genetic engineering context module
to receive a query sequence for a biological specimen
transmit an identification of the presence of genetic engineering in the biological specimen in response to a determination that the match exists
The element of receiving a query sequence is considered to be a data gathering element because it gathers the sequence data on which the judicial exceptions are performed. Data gathering steps are not abstract ideas but represent extra-solution activity, as said steps collect the data needed to carry out the abstract idea. Data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g)). The element of indicating the presence is an ancillary step to the judicial exceptions and simply displays the results of the judicial exception. It is thus an extra-solution step and does not integrate the judicial exceptions into a practical application. The element of a computing device does not describe any specific computation steps by which the computer parts perform or carry out the abstract idea, nor do they provide any details of how specific structures of the computer are used to implement the function. The claims state nothing more than a generic computer, hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not integrate that abstract idea into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc. … are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linked the use of the judicial exception to the technological environment of a computer (see MPEP 2106.05(f)).
Dependent claims 24 and 27 recite further steps of data gathering or limiting the data gathered. As such, these claims do not integrate the judicial exceptions into a practical application (MPEP 2106.05(g)).
With respect to step (2B): Because the claims recite an abstract idea, and do no integrate that abstract idea into a practical application, the claims lack a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements above do not rise to the level of significantly more than the judicial exception. As directed in the MPEP at 2106.05(d)(I), determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to claims 1 and 9: The additional elements of --receiving a query sequence for a biological specimen, transmitting to the client device over the network, and a computing device do not rise to the level of significantly more than the judicial exception. With respect to Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546 and University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014), sequence data of a biological specimen, such as nucleic acid sequence data is routine and conventional. With respect to indicating presence of the genetic engineering context signature and the computing device, as exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the abstract idea (see MPEP 2105(b)I-III). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claims 24 and 27: The additional element of the biological specimen being a pathogenic organism does not rise to the level of significantly more than the judicial exception. The prior art to Diggans et al. (US 20170357752 A1, published December 2017, IDS reference) discloses that knowledge about individual proteins and biological system capable of posting potential threats to public safety and/or the environment has been increasing tremendously (paragraph [0002]). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
The claims have all been examined to identify the presence of one or more judicial exceptions. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether the additional limitations integrate the judicial exception into a practical application. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether those additional limitations provide an inventive concept which provides significantly more than those exceptions. Individually, the limitations of the claims and the claims as a whole have been found to not meet the eligibility requirements.
Response to Arguments
Applicant states that “neither ‘regions of interest in the query sequence’ that each comprise ‘part of a whole protein translated region’ nor ‘whether a match for a genetic engineering context signature exists in the query sequence adjacent to any of the one or more regions of interest of the query sequence’ could practically be determined in the human mind. As such, the alleged abstract idea(s) pointed to in the Office Action cannot fairly be considered ‘mental processes.’”
It is respectfully submitted that this is not persuasive. A step of “determining one or more regions of interest” is able to be performed mentally, and furthermore, determining whether a match for a genetic engineering context signature exists is as well. There is no requirement to the size of the sequence query, and thus it is reasonable to assume that one of ordinary skill could mentally process a sequence to determine if there is a match for a sequence found in a database. Thus, the rejection under 35 USC 101 is maintained.
Furthermore, Applicant likens the instant claims to Enfish and states that “searching an entire whole protein translated region for genetic engineering context signatures would consume significant computer time and resources. The present invention, however, significantly improves the operation of the bioinformatics software and the computing device running that software by initially determining specific regions of interest that each comprise a part of the whole protein translated region. Next, the software searches for genetic engineering context signatures adjacent to the regions of interest, specifically with searches targeted at a predetermined search range upstream or downstream of each region of interest. The predetermined search range is particular to a context signature type of the sequence selected from the database (i.e., the genetic engineering context signatures being searched). By targeting the searches for genetic engineering context signatures in this manner, the claimed method significantly and practically improves the operation of the computing device executing it.”
It is respectfully submitted that this is not persuasive. An improvement to software, as claimed in the arguments, is not an improvement that is capable of integrating the claims into a practical application. The improvement must be a meaningful application that uses the judicial exception in a way beyond generally linking the use of the judicial exceptions to a technological environment . These claims, which may be applied as improved software, comprise abstract ideas performed on a computer. Improvement in abstract ideas is not able to integrate the judicial exceptions into a practical application. The instant claims do not meaningfully use any of the results of the judicial exceptions. The claims only require that a confirmation of the identification of genetic engineering is transmitted, which is thus an ancillary step and represents an extra-solution step (see MPEP 2106.05(g)). Thus, the rejection under 35 USC 101 is maintained.
Finally, Applicant states that “The foregoing features also present an inventive concept that is not well-understood, routine, conventional activity in the relevant field. The Federal Circuit case of BASCOM Glob. Internet Servs., Inc. v. AT&T Mobility LLC, 827 F.3d 1341 (Fed. Cir. 2016) is instructive. Finding the claimed software-based invention patent eligible in BASCOM, the Federal Circuit noted, ‘[t]he inventive concept inquiry requires more than recognizing that each claim element, by itself, was known in the art. As is the case here, an inventive concept can be found in the non-conventional and non-generic arrangement of known, conventional pieces.’ BASCOM, 827 F.3d at 1350. Applicant’s claims involve an inventive concept at least because the prior art fails to teach or suggest the claimed inventions. As detailed below, the prior art fails to teach all of the elements of the pending claims. The Office Action has not established that the specific features recited in the claims were ‘well-understood, routine and conventional activities previously known to the industry.’”
It is respectfully submitted that this is not persuasive. The steps used by the Office to determine subject matter eligibility under 35 USC 101 are outlined in the MPEP at 2106. It is the additional elements that are examined to determine if there is an inventive concept (MPEP 2106.05.A i-vi). Thus, it is not the conventionality of all claim limitations that is considered in Step 2B, and the claims overcoming prior art under USC 102 or 103 does not indicate eligibility under Step 2B of the 35 USC 101 analysis. The additional elements in the independent claims comprise receiving a query sequence, transmitting an identification of the presence of genetic engineering, and a computing device to perform the method. With respect to Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546 and University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014), sequence data of a biological specimen, such as nucleic acid sequence data is routine and conventional. With respect to indicating presence of the genetic engineering context signature and the computing device, as exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the abstract idea (see MPEP 2105(b)I-III). Thus, the rejection under 35 USC 101 is maintained.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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 1, 5, 6, 8, 9, 12, 21, 22, 24, 25, 27, 28, 31, and 33 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Nielsen et al. (“Deep learning to predict the lab-of-origin of engineered DNA”, Nature Communications, 2018). This is a new grounds of rejection.
Regarding claims 1 and 9, Nielsen et al. teaches a method and computing system for identifying the presence of genetic engineering attributed to a particular lab (Abstract) comprising:
receiving a query sequence for the biological specimen: Nielsen et al. teaches a computing system in which a query DNA sequence associated with a plasmid is input (Figure 1a);
determining one or more regions of interest in the query sequence, wherein each region of interest comprises part of a whole protein translated region; and determining whether a match for a genetic engineering context signature exists in the query sequence adjacent to any of the one or more regions of interest of the query sequence, wherein the genetic engineering context signature comprises a sequence selected from a database of sequences indicative of genetic engineering, and wherein determining whether the match for the genetic engineering context signature exists adjacent to any of the one or more regions of interest comprises searching upstream or downstream of each region of interest over a predetermined search range that is particular to a context signature type of the sequence selected: Nielsen et al. teaches plasmid sequence data deposited into databases (page 3, column 1, paragraphs 1 and 2), and teaches inputting these sequences into a convolutional neural network (page 3, column 1, paragraph 4); Nielsen et al. teaches tools such as the neural network or BLAST which compare input sequences to sequences from the databases and thus identify which lab a sequence was engineered by (page 3, column 2, paragraphs 3 and 4); Nielsen et al. teaches a method of determining what sequence the neural network uses to identify the lab-of-origin, and determines context signatures adjacent to the regions of interest in the plasmid (page 4, column 2), such as a pair of restriction sites adjacent to a plasmid insert, that contribute to the neural network identifying the origin of the sequence (page 5, column 1, paragraph 4);
transmitting an identification of the presence of genetic engineering the biological specimen in response to determining that the match exists: Nielsen et al. teaches an output indicating the probability of which lab the sequence originated from due to determining a match (Figure 3b and c).
Furthermore, Nielsen et al. teaches a computer-implemented method (see Figure 1) and thus inherently teaches the claimed computing device.
Regarding claims 5 and 12, the claims are directed to the genetic engineering context signature comprises an upstream regulatory element, a downstream regulatory element, or a tag. Nielsen et al. teaches the method of claim 1 and the device of the claim 9. Nielsen et al. teaches that the context signature present in an engineered plasmid comprises a tag (page 5, column 1, paragraph 3).
Regarding claims 6 and 22, the claims are directed to the genetic engineering context signature comprising an upstream regulatory element, wherein the upstream regulatory element comprises a promoter, a ribosome binding site, an operator that contributes to transcript regulatory, or an enhancer. Nielsen et al. teaches the method of claim 5 and the device of the claim 12. Nielsen et al. teaches CNNs that analyze DNA sequences to identify promoters and regulator binding sites (page 2, column 2, paragraph 2).
Regarding claims 8 and 21, the claims are directed to the genetic engineering context signature comprising a tag, wherein the tag comprises a purification/epitope tag, a cleavage sequence, or a targeting sequence. Nielsen et al. teaches the method of claim 5 and the device of claim 12. Nielsen et al. teaches that the context signature present in an engineered plasmid comprises an affinity tag (epitope tag) (page 5, column 1, paragraph 3).
Regarding claims 24 and 27, the claims are directed to the biological specimen is a pathogenic organism. Nielsen et al. teaches the method of claim 1 and the device of the claim 9. Nielsen et al. teaches that the genetically engineered specimens may be pathogenic organisms (Abstract; page 2, column 1).
Regarding claims 25 and 28, the claims are directed to the sequence of the genetic engineering signature regulating transcription of an associated region of interest of the query sequence. Nielsen et al. teaches the method of claim 1 and the device of the claim 9. Nielsen et al. teaches CNNs that analyze DNA sequences to identify promoters and regulator binding sites (page 2, column 2, paragraph 2).
Regarding claims 31 and 33, the claims are directed to using the identification of the presence of genetic engineering in the biological specimen to assist in determining culpability for a release of the biological specimen. Nielsen et al. teaches the method of claim 1 and the device of the claim 9. Nielsen et al. teaches using the identification of the genetic engineering sequences to assist in determining the lab-of-origin of the specimen (Abstract).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 7, 23, 26, and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Nielsen et al., as applied to claims 1, 5, 6, 8, 9, 12, 21, 22, 24, 25, 27, 28, 31, and 33 in the 102 rejection above, in view of Bonyhadi et al. (US 2019/0345543 A1, published November 2019, cited in prior Office Action). This is a new grounds of rejection.
Regarding claims 7 and 23, the claims are directed to the genetic engineering context signature comprising a downstream regulatory element, wherein the downstream regulatory element comprises a terminator, a polyA site, a woodchuck hepatitis virus posttranscriptional regulatory element (WPRE), a C-terminal expansion (CTE), or a long terminal repeat (LTR). Nielsen et al. teaches the method of claim 5 and the device of the claim 12.
Nielsen et al. does not teach the claim element of the genetic engineering context signature comprising a downstream regulatory element, wherein the downstream regulatory element comprises a terminator, a polyA site, a woodchuck hepatitis virus posttranscriptional regulatory element (WPRE), a C-terminal expansion (CTE), or a long terminal repeat (LTR).
However, Bonyhadi et al. teaches epigenetic analysis of cell therapy and related methods. Bonyhadi et al. also teaches a context signature of the genetically engineered cell being upstream or downstream of the genomic region of interest, such as a promoter, enhancer, or termination site (paragraph [0058]). Bonyhadi et al. also teaches the context signature of the genetically engineered cell comprising a promoter or an enhancer (paragraph [0058]).
Regarding claims 26 and 29, the claims are directed to a start of the predetermined search range being no more than 800 base pairs upstream of each region of interest and an end of the predetermined search range being no more than 1200 base pairs downstream of each region of interest. Nielsen et al. teaches the method of claim 1 and the device of the claim 9. Nielsen et al. also teaches a 12bp context sequence adjacent to a plasmid insert (page 5, column 1, paragraph 4).
Nielsen et al. does not specifically teach the claim element of a start of the predetermined search range being no more than 800 base pairs upstream of each region of interest and an end of the predetermined search range being no more than 1200 base pairs downstream of each region of interest.
Bonyhadi et al. also teaches a context signature of the genetically engineered cell being upstream or downstream of the genomic region of interest, such as a promoter, enhancer, or termination site (paragraph [0058]) and teaches a predetermined panel including a predetermined number of genomic regions such as 2 to 50, 2 to 20, 2 to 10, etc. (paragraph [0068]), and steps for searching for motifs, enriched transcription factor binding motifs (paragraph [0175]).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have incorporated the context signatures of the genetically engineered cells of Bonyhadi et al. to the method of Nielsen et al. because Nielsen et al. is directed to identifying aspects of genetically engineered DNA that determine the designer of the sequence (Abstract) and Bonyhadi et al. teaches identifying the properties and assessing gene regions of an engineered cell (Abstract). Thus, one of ordinary skill in the art would have had a reasonable expectation of success in combining the prior art elements because the prior art references are both directed to analysis of genetically engineered cells. Thus, it would be obvious to one of ordinary skill in the art that a context signature of a genetically engineered cell used to identify the genetic engineering would comprise any of these regulatory elements.
Claims 30 and 32 are rejected under 35 U.S.C. 103 as being unpatentable over Nielsen et al., as applied to claims 1, 5, 6, 8, 9, 12, 21, 22, 24, 25, 27, 28, 31, and 33 in the 102 rejection above, in view of Diggans (US 20170357752 A1, published December 2017, IDS reference). This is a new grounds of rejection.
Regarding claims 30 and 32, the claims are directed to preventing a release of the biological specimen in response to the identification of the presence of genetic engineering in the biological specimen. Nielsen et al. teaches the method of claim 1 and the device of the claim 9. Nielsen et al. teaches engineered pathogens used as biological weapons (page 2, column 1).
Nielsen et al. does not specifically teach the claim element of prevent a release of the biological specimen.
However, Diggans teaches systems and methods for automated annotation and screening of biological sequences. Diggans teaches systems and methods for designing and synthesizing biological sequences or constructs with enhanced biosafety and biosecurity including preventative measures aimed to prevent contact with harmful biological agents and preventative measures aimed to prevent the use or spread of harmful biological agents (paragraph [0083]).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have incorporated preventing release of a biological specimen to the method of Nielsen et al. because Nielsen et al. is directed to identifying culpability of genetic engineered DNA due to the possibility of malicious intent (Abstract) and Diggans teaches preventative measures to prevent the spread of harmful biological agents (paragraph [0083]) through the screening of biological sequences. Thus, one of ordinary skill in the art would have had a reasonable expectation of success in combining the prior art references as both references discuss analysis of genetically engineered sequences, and it would have been obvious to do so as one of ordinary skill in the art would be motivated to prevent the release of an identified engineered organism deemed to be harmful.
Response to Arguments
Applicant states that “Bonyhadi contains no teachings regarding identifying the presence of genetic engineering in a biological specimen. Bonyhadi discloses methods of epigenetic and/or epigenomic analyses of cells in connection with methods for preparing engineered cells for cell therapy and/or predicting a response to cell therapy”.
It is acknowledged that this is persuasive. Bonyhadi does not appear to teach the instant claims of identifying genetic engineering as recited in the instant claims. A new grounds of rejection has been set forth.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to EMILIE A NEULEN whose telephone number is (571)272-7543. The examiner can normally be reached 9am - 5pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D Riggs can be reached at (571)270-3062. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/E.A.N./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686