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 .
Election/Restrictions
Applicant’s election without traverse of Group I, claims 3-5, 8, 10-12, 15, 19, 28-29, 52, 56, and 60-61 drawn to a method for providing traceability of biological material in the reply filed on 3/24/2026 is acknowledged.
Claims 62-70 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected inventions, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 3/24/2026.
Claim Status
Claims 1-2, 6-7, 9, 13-14, 16-18, 20-27, 30-51, 53-55, and 57-59 are cancelled.
Claims 60-70 are newly added.
Claims 3-5, 8, 10-12, 15, 19, 28-29, 52, 56, and 60-70 are pending.
Claims 3-5, 8, 10-12, 15, 19, 28-29, 52, 56, and 60-61 are examined on the merits.
Claims 62-70 are withdrawn.
Priority
The instant application is a 371 of PCT/CA2020/051622 filed on 11/26/2020, which claims priority to U.S. Provisional Application 62/940,587 filed on 11/26/2019. At this point in examination, the effective filing date of claims 3-5, 8, 10-12, 15, 19, 28-29, 52, 56, and 60-70 is 11/26/2019.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 5/26/2022, 2/28/2024, and 3/18/2025 are in compliance with the provisions of 37 CFR 1.97. A signed copy of the corresponding 1449 form has been included with this Office Action.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Specification
There are hyperlinks in the following locations of the instant specification:
pg. 48, para. 1, line 5
pg. 57, para. 2, line 7-9
pg. 58, para. 1, line 4
pg. 59, para. 1, line 4
pg. 71-72, para. 3, lines 8 and 10
pg. 84, lines 3, 7-8, 14, and 20
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Objections
Claims 29 and 60-61 are objected to because of the following informalities:
Claim 29, line 4 recites "searching the DUID database for an exact match to the query DUID". Insert "or" before this line.
Claim 60, line 2 recites “one more innocuous site”, which should read “one or more innocuous sites”.
Claim 61, line 2 recites “one or more innocuous site”, which should read “one or more innocuous sites”.
These are typographical errors. Appropriate correction is required.
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.
Claims 3 and 8 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 term “thereby providing traceability” in claim 3, line 19 is a relative term which renders the claim indefinite. The term “thereby providing traceability” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear if there is an active step of "reading the DNA unique identifier sequence", "retrieving the corresponding database entry", and "providing the identification and/or tracking information". The specification is also silent as to whether these steps are acted on or not. One skilled in the art would not recognize that the steps in providing traceability are active steps. Therefore, claim 3 is rendered indefinite and rejected under 35 U.S.C. 112(b).
Claim 8 recites the limitation "producing a biological material from the biological entity" in line 2. There is insufficient antecedent basis for this limitation in the claim. It is unclear if there is an active producing step in claim 3, which it depends on. The rejection might be overcome by amending the claim to introduce clear antecedent basis for “producing a biological material”. For compact prosecution, it is assumed that the preceding suggested will be implemented.
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 3-5, 8, 10-12, 15, 19, 28-29, 52, 56, and 60-61 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite: (a) mathematical concepts, (e.g., mathematical relationships, formulas or equations, mathematical calculations); and (b) mental processes, i.e., concepts performed in the human mind, (e.g., observation, evaluation, judgement, opinion).
Subject matter eligibility evaluation in accordance with MPEP 2106:
Eligibility Step 1: Claims 3-5, 8, 10-12, 15, 19, 28-29, 52, 56, and 60-61 are directed to a method (process) for providing traceability of biological material. Therefore, these claims are encompassed by the categories of statutory subject matter, and thus satisfy the subject matter eligibility requirements under Step 1.
[Step 1: YES]
Eligibility Step 2A: First, it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception.
Eligibility Step 2A, Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes whether the claim recites a judicial exception, i.e., whether a law of nature, natural phenomenon, or abstract idea is set forth described in the claim.
Claims 3, 10, 28-29, and 56 recite the following steps which fall within the mental processes and/or mathematical concepts groups of abstract ideas, as noted below.
Independent claim 3 further recites:
determining the sequence of at least one DNA unique identifier sequence within the genomic DNA of a biological entity, wherein the biological entity comprises a plant cell, a fungal cell, an animal cell, a virus, or a bacterial cell (i.e., mental processes);
verifying presence of the DNA unique identifier sequence in the genomic DNA (i.e., mental processes);
comparing the sequence of the DNA unique identifier sequence with a database to confirm that the DNA unique identifier sequence is not already used in the database (i.e., mental processes);
associating the DNA unique identifier sequence with identification and/or tracking information for the biological material (i.e., mental processes).
Dependent claim 10 further recites:
comparing the DNA unique identifier sequence to the database (i.e., mental processes).
Dependent claim 28 further recites:
searching at the computing device a DUID database storing a plurality of DUIDs in association with respective biological material information for a match to the received DUID (i.e., mental processes);
searching at the computing device the DUID database for a match to the received query DUID (i.e., mental processes).
Dependent claim 29 further recites:
searching the DUID database for an exact match to the received DUID (i.e., mental processes);
searching the DUID database for an exact match to the query DUID (i.e., mental processes);
if an exact match is not found, performing an alignment/identity search for DUIDs stored in the DUID database that are a close match to the received DUID or the query DUID (i.e., mental processes).
Dependent claim 56 further recites:
searching for the DNA unique identifier sequence in a database (i.e., mental processes).
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification. As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pencil and paper, and therefore recite judicial exceptions from the mental process grouping of abstract ideas. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind. Dependent claims 11-12, 15, 19, and 60-61 recite information further limiting the judicial exceptions indicated above.
Therefore, claims 3, 10, 28-29, and 56 recite an abstract idea.
[Step 2A, Prong One: YES]
Eligibility Step 2A, Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that, when examined as a whole, integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed 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 fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)).
The judicial exceptions identified in Eligibility Step 2A, Prong One are not integrated into a practical application because of the reasons noted below.
Claim 4 recites inserting at least one DNA unique identifier sequence within the genomic DNA of a biological entity, or modifying a pre-existing identifier sequence within the genomic DNA of a biological entity by gene editing to create a DNA unique identifier sequence within the genomic DNA of the biological entity, thereby providing identification thereof. Gene editing is used to insert a DNA identifier sequence in genomic DNA or modify a pre-existing DNA identifier sequence to be inserted in genomic DNA, which provides identification for further analysis. Data gathering steps are extra-solution activity as they collect the data needed to carry out the JE. It does not impose any meaningful limitation on the JE or how the JE is performed (MPEP 2106.04/.05, citing Intellectual Ventures LLC v. Symantee Corp, McRO, TLI communications, OIP Techs. Inc. v. Amason.com Inc., Electric Power Group LLC v. Alstrom S.A.). Therefore, the claimed additional element does not integrate the abstract ideas into a practical application.
Claims 10 and 56 recite amplifying the at least one DNA unique identifier sequence within the genomic DNA from the biological material and sequencing the DNA unique identifier sequence. It is notable that mere physicality or tangibility of an additional element or elements is not a relevant consideration in Step 2A Prong Two. As the Supreme Court explained in Alice Corp., mere physical or tangible implementation of an exception does not guarantee eligibility. Alice Corp. Pty. Ltd. v. CLS Bank Int’l, 573 U.S. 208, 224, 110 USPQ2d 1976, 1983-84 (2014) ("The fact that a computer ‘necessarily exist[s] in the physical, rather than purely conceptual, realm,’ is beside the point"). See MPEP 2106.04(d)(I), citing Genetic Technologies Ltd. v. Merial LLC, 818 F.3d 1369, 1377, 118 USPQ2d 1541, 1547 (Fed. Cir. 2016) (steps of DNA amplification and analysis are not "sufficient" to render claim 1 patent eligible merely because they are physical steps). Therefore, the claimed additional element does not integrate the abstract ideas into a practical application.
Claims 3, 5, 8, 10, 28-29, 52, and 56 recite the additional non-abstract elements of data gathering:
providing an indication of acceptability to produce a biological material from the biological entity, the biological material comprising genomic DNA from the biological entity, wherein the biological material comprises a food, a plant-based material, a fungus-based material, an animal-based material, a virus-based material, or a bacterial-based material (claim 3);
inputting the sequence of the at least one DNA unique identifier sequence into a database entry of the database (claim 3);
providing the at least one DNA unique identifier sequence for the insertion within the genomic DNA of the biological entity (claim 5);
wherein producing a biological material from the biological entity comprising propagating the biological entity (claim 8);
receiving or providing a sample comprising genomic DNA from the biological material (claim 10);
retrieving the database entry corresponding with the DNA unique identifier sequence, the database entry providing identification and/or tracking information for the biological material (claim 10);
receiving at a computing device the DNA-unique identifier sequence (DUID) extracted from a known biological material (claim 28);
if the search of the DUID database fails to provide a match to the received DUID, storing in the DUID database the received DUID in association with biological material information associated with the known biological material (claim 28);
subsequent to storing the received DUID and with information associated with the known biological material in the DUID database, receiving at the computing device a query DUID extracted from an unknown biological material (claim 28);
if the search of the DUID provides a match to the received query DUID, returning in response to the received query DUID the biological information stored in association with the DUID matching the query DUID (claim 28);
if the search provides a close match to the query DUID, storing the query DUID in association with the DUID that is a close match to the query DUID (claim 29);
producing the biological material from the biological entity, the biological material comprising genomic DNA from the biological entity (claim 52);
providing an indication of acceptability to produce the biological material from the biological entity, the biological material comprising genomic DNA from the biological entity (claim 52);
receiving or providing a sample from the product of interest, wherein the product of interest comprises food, an agricultural product, a pharmaceutical drug, a retail product, textiles, commodities, chemicals, or another supply chain item, the sample comprising genomic DNA from a biological material part of, mixed with, or otherwise associated with the product of interest (claim 56);
retrieving a database entry corresponding with the DNA unique identifier sequence, the database entry providing identification and/or tracking information for the product of interest, wherein the identification and/or tracking information of the database entry comprises supply chain information for the product of interest (claim 56).
which are each a data gathering step, or a description of the data gathered.
Data gathering steps are not an abstract idea, they are extra-solution activity, as they collect the data needed to carry out the JE. The data gathering does not impose any meaningful limitation on the JE, or how the JE is performed. The additional limitation (data gathering) must have more than a nominal or insignificant relationship to the identified judicial exception. (MPEP 2106.04/.05, citing Intellectual Ventures LLC v. Symantee Corp, McRO, TLI communications, OIP Techs. Inc. v. Amason.com Inc., Electric Power Group LLC v. Alstrom S.A.).
Thus, the additionally recited elements merely invoke a computer as a tool, and/or amount to insignificant extra-solution data gathering activity, and as such, when all limitations in claims 3-5, 8, 10-12, 15, 19, 28-29, 52, 56, and 60-61 have been considered as a whole, the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application. Claims 3-5, 8, 10, 28-29, 52, and 56 contain additional elements that would not integrate a judicial exception into a practical application and are further probed for inventive concept in Step 2B.
[Step 2A, Prong Two: NO]
Eligibility Step 2B: Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are probed for 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 amount to significantly more than the judicial exception (MPEP 2106.05A i-vi).
The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because of the reasons noted below.
With respect to claims 3, 5, 8, 10, 28-29, 52, and 56: The limitations identified above as non-abstract elements (EIA) related to data gathering do not rise to the level of significantly more than the judicial exception. Activities such as data gathering do not improve the functioning of a computer, or comprise an improvement to any other technical field. The limitations do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide an unconventional step (citing McRO and Trading Technologies Int’l v. IBG). Data gathering steps constitute a general link to a technological environment. Simply appending well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception are insufficient to provide significantly more (as discussed in Alice Corp.,).
The additional element of inserting at least one DNA unique identifier sequence within the genomic DNA of a biological entity, or modifying a pre-existing identifier sequence within the genomic DNA of a biological entity by gene editing to create a DNA unique identifier sequence within the genomic DNA of the biological entity (claim 4) is conventional. Evidence for conventionality is shown by National Human Genome Research Institute (NIH, 2019, 1-3). National Human Genome Research Institute reviews “Genome editing technologies enable scientists to make changes to DNA, leading to changes in physical traits, like eye color, and disease risk. Scientists use different technologies to do this. These technologies act like scissors, cutting the DNA at a specific spot. Then scientists can remove, add, or replace the DNA where it was cut.” (pg. 1, para. 1). This shows that a DNA sequence can be inserted into the genomic DNA, which makes it a conventional practice in the art.
The additional element of amplifying the at least one DNA unique identifier sequence within the genomic DNA from the biological material and sequencing the DNA unique identifier sequence (claims 10 and 56) is conventional. The courts have recognized that amplifying and sequencing nucleic acid sequences is a laboratory technique that is well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as an insignificant extra-solution activity. MPEP 2106.05(d)(II), citing University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014).
[Step 2B: NO]
Therefore, claims 3-5, 8, 10-12, 15, 19, 28-29, 52, 56, and 60-61 are patent ineligible under 35 U.S.C. § 101.
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.
Claims 3, 8, 10, 12, 15, 52, and 56 are rejected under 35 U.S.C. 103 as being unpatentable over Nicolè et al. (Food Technology and Biotechnology, 2012, 50(4), 387-398), in view of Barcaccia et al. (Diversity, 2016, 8(1), 1-16), as provided in the IDS filed 5/26/2022, and Stoeckle et al. (Scientific Reports, 2011, 42(1), 1-7).
With respect to claim 3:
Regarding the recited determining the sequence of at least one DNA unique identifier sequence within the genomic DNA of a biological entity, wherein the biological entity comprises a plant cell, a fungal cell, an animal cell, a virus, or a bacterial cell, Nicolè et al. discloses at least one DNA barcode region was amplified in the total genomic DNA extracted and purified from 37 seafood samples (pg. 388, col. 2, para. 2, lines 1-4; pg. 388, col. 2, para. 3, lines 1-6). The seafood samples are the biological entities comprising of an animal cell.
Regarding the recited validating identification of the biological entity by: verifying presence of the DNA unique identifier sequence in the genomic DNA, Nicolè et al. discloses successful amplification of the DNA barcode region in the isolated genomic DNA (pg. 390, col. 2, para. 2, lines 1-5; pg. 388, col. 2, para. 3, lines 1-6). This suggests confirmation of the presence of the identifier sequence through PCR amplification. Also, further discloses that conventional DNA barcoding is an efficient tool used to identify food components and validate label information contents (pg. 396, col. 1, para. 3, lines 1-4).
Regarding the recited comparing the sequence of the DNA unique identifier sequence with a database to confirm that the DNA unique identifier sequence is not already used in the database, Nicolè et al. discloses conducting a similarity analysis and a phylogenetic approach to compare amplified sequences to reference sequences in the GenBank and BOLD databases (pg. 390, col. 1, para. 2, lines 1-4; pg. 390, col. 1, para. 3, lines 1-4). This suggests making comparisons between the identifier sequence and sequences of a database. Also, further discloses two tiers of BOLD database comparisons, where if the first tier of comparisons to a database of validated sequences reports no match, move on to comparisons with cox1 barcode sequences, which includes non-validated records that have no species identification (pg. 390, col. 1, para. 3, lines 6-13). This teaches that the comparisons are used to check if the identifier sequence is not already in the database of validated sequences.
Regarding the recited inputting the sequence of the at least one DNA unique identifier sequence into a database entry of the database, and associating the DNA unique identifier sequence with identification and/or tracking information for the biological material, Nicolè et al. discloses depositing mtDNA sequences in the NCBI database under GenBank accession numbers (pg. 390, col. 2, para. 2, lines 11-13). This indicates inputting the identifier sequence into a database and associating the sequence with an identification number.
Nicolè et al. does not disclose a method for providing traceability of biological material.
However, Barcaccia et al. discloses DNA barcoding, a method that uses a short genetic marker from a standard part of the genome of an organism’s DNA to identify it as belonging to a particular individual (pg. 1, para. 2, lines 1-3). This suggests traceability of biological material by identifying a DNA barcode as linked to an organism.
Regarding the recited providing an indication of acceptability to produce a biological material from the biological entity, the biological material comprising genomic DNA from the biological entity, wherein the biological material comprises a food, a plant-based material, a fungus-based material, an animal-based material, a virus-based material, or a bacterial-based material, Nicolè et al. discloses that conventional DNA barcoding is an efficient tool used to identify food components and validate label information contents (pg. 396, col. 1, para. 3, lines 1-4).
Barcaccia et al. discloses that DNA barcoding is an affordable method used for verification in particular foodstuff cases (e.g., when recall of a batch is required) or authentication in specific products (e.g., any transformed or processed product), which ensures efficient recall and can prevent from recalling safe batches (pg. 12-13, para. 6, lines 1-11). This suggests that DNA barcoding can verify or authenticate the production of biological material comprising of food or animal-based material.
Nicolè et al. does not disclose thereby providing traceability of the biological material by reading the DNA unique identifier sequence in the biological material and retrieving the corresponding database entry providing the identification and/or tracking information for the biological material.
However, Barcaccia et al. discloses DNA barcoding, a method that uses a short genetic marker from a standard part of the genome of an organism’s DNA to identify it as belonging to a particular individual (pg. 1, para. 2, lines 1-3). This suggests traceability of biological material by identifying a DNA barcode as linked to an organism.
Barcaccia et al. does not disclose retrieving the corresponding database entry providing the identification and/or tracking information for the biological material.
However, Stoeckle et al. discloses recovering rbcL and matK barcodes from tea products, obtaining readable sequences from those barcodes, performing BLAST search through GenBank and Barcode of Life databases, and recording closest matches in each database (pg. 2, col. 1-2, para. 3, lines 1-12). This suggests using the DNA barcoding method to provide traceability of biological material by reading identifier sequences through BLAST search and retrieving the corresponding database entry providing identification for the biological material.
It would have been prima facie obvious to one of ordinary skill in the art to modify DNA barcoding disclosed by Nicolè et al. to incorporate the teachings disclosed by Barcaccia et al. and Stoeckle et al. One would be motivated to incorporate the teachings because Barcaccia et al. discloses that DNA barcoding is reproducible and testable as long as the link between DNA test sequences and reference specimens is supported, and also verifiable at any time and by any researcher (pg. 11, para. 4, lines 1-3). This means that DNA barcoding is reproducible, testable, and verifiable, emphasizing the flexibility of the method disclosed by Nicolè et al. Stoeckle et al. also discloses recovering rbcL or matK barcodes from 90% of commercial tea products using a single set of primers for each region (pg. 5, col. 1, para. 1, lines 1-6). This suggests that, if incorporated into the method disclosed by Nicolè et al., barcode sequences will be effectively recovered from majority of the samples. There is a likelihood of success, since these are all methods of DNA barcoding and are well known in the field of molecular biology.
With respect to claim 8:
Nicolè et al. and Stoeckle et al. do not disclose wherein producing a biological material from the biological entity comprising propagating the biological entity.
However, Barcaccia et al. discloses that DNA barcoding is an affordable method used for verification in particular foodstuff cases (e.g., when recall of a batch is required) or authentication in specific products (e.g., any transformed or processed product), which ensures efficient recall and can prevent from recalling safe batches (pg. 12-13, para. 6, lines 1-11). This suggests that batches of biological entities are produced or recalled based on the verification or authentication of the products.
With respect to claim 10:
Regarding the recited receiving or providing a sample comprising genomic DNA from the biological material, Nicolè et al. discloses extracting and purifying genomic DNA from 37 seafood samples collected from markets and groceries of North-Eastern Italy (pg. 388, col. 2, para. 2, lines 1-4; pg. 388, col. 2, para. 3, lines 1-5). This describes receiving a sample comprising genomic DNA.
Regarding the recited amplifying the at least one DNA unique identifier sequence within the genomic DNA from the biological material and sequencing the DNA unique identifier sequence, Nicolè et al. discloses amplifying and sequencing the DNA barcode regions within the genomic DNA from the seafood samples (pg. 388, col. 2, para. 3, lines 1-6; pg. 389, col. 2, para. 1, lines 1-4). This describes amplifying and sequencing at least one identifier sequence.
Nicolè et al. and Barcaccia et al. do not disclose wherein reading the DNA unique identifier sequence in the biological material and retrieving the corresponding database entry.
However, Stoeckle et al. discloses recovering rbcL and matK barcodes from tea products, obtaining readable sequences from those barcodes, performing BLAST search through GenBank and Barcode of Life databases, and recording closest matches in each database (pg. 2, col. 1-2, para. 3, lines 1-12). This suggests reading identifier sequences through BLAST search and retrieving the corresponding database entry providing identification for the biological material.
Nicolè et al. and Barcaccia et al. do not disclose comparing the DNA unique identifier sequence to the database and retrieving the database entry corresponding with the DNA unique identifier sequence, the database entry providing identification and/or tracking information for the biological material.
However, Stoeckle et al. discloses recovering rbcL and matK barcodes from tea products, obtaining readable sequences from those barcodes, performing BLAST search through GenBank and Barcode of Life databases, and recording closest matches in each database (pg. 2, col. 1-2, para. 3, lines 1-12). This suggests comparing the identifier sequence to the sequences of the databases through BLAST search and retrieving the corresponding database entry providing identification for the biological material.
With respect to claim 12:
Nicolè et al. and Barcaccia et al. do not disclose wherein the DNA unique identifier sequence comprises a sequence of up to about 1500nt in length; up to about 1000nt in length; about 200nt to about 600nt in length; about 200nt to about 400nt in length; or about 400nt to about 600nt in length, and is flanked by one or more primer annealing sequences for PCR amplification of the DNA unique identifier sequence, sequencing of the DNA unique identifier sequence, or both.
However, Stoeckle et al. discloses that the rbcL and matK barcode sequences are about 550 bp and 790 bp, respectively (pg. 1, para. 4, lines 1-3). Because rbcL and matK genes are double-stranded, converting from base pairs to number of nucleotides in length gives
550
x
2
=
1100
nt and
790
x
2
=
1580
nt, respectively. Also, further discloses the PCR amplification procedure, which includes flanking the barcode sequences with primer annealing sequences and bi-directional sequencing (pg. 6, col. 2, para. 5-6).
With respect to claim 15:
Regarding the recited wherein the identification and/or tracking information of the database entry comprises supply chain information for the biological material, source-of-origin information for the biological material, grower, region, batch, lot, date, relevant supply chain information, or any combinations thereof, Nicolè et al. discloses that the seafood samples were labeled with the genus and species, common name, and capture location (pg. 388, col. 2, para. 2, lines 4-6). This indicates that the identification information of the database entry for the biological material comprises of source-of-origin information.
With respect to claim 52:
Nicolè et al. and Stoeckle et al. do not disclose producing the biological material from the biological entity, the biological material comprising genomic DNA from the biological entity.
However, Barcaccia et al. discloses that DNA barcoding is an affordable method used for verification in particular foodstuff cases (e.g., when recall of a batch is required) or authentication in specific products (e.g., any transformed or processed product), which ensures efficient recall and can prevent from recalling safe batches (pg. 12-13, para. 6, lines 1-11). This suggests that batches of biological material in biological entities are produced or recalled based on the verification or authentication of the products.
Stoeckle et al. do not disclose providing an indication of acceptability to produce the biological material from the biological entity, the biological material comprising genomic DNA from the biological entity.
However, Nicolè et al. discloses that conventional DNA barcoding is an efficient tool used to identify food components and validate label information contents (pg. 396, col. 1, para. 3, lines 1-4).
Barcaccia et al. discloses that DNA barcoding is an affordable method used for verification in particular foodstuff cases (e.g., when recall of a batch is required) or authentication in specific products (e.g., any transformed or processed product), which ensures efficient recall and can prevent from recalling safe batches (pg. 12-13, para. 6, lines 1-11). This suggests that DNA barcoding can verify or authenticate the production of biological material.
With respect to claim 56:
Regarding the recited receiving or providing a sample from the product of interest, wherein the product of interest comprises food, an agricultural product, a pharmaceutical drug, a retail product, textiles, commodities, chemicals, or another supply chain item, the sample comprising genomic DNA from a biological material part of, mixed with, or otherwise associated with the product of interest, Nicolè et al. discloses extracting and purifying genomic DNA from 37 seafood samples collected from markets and groceries of North-Eastern Italy (pg. 388, col. 2, para. 2, lines 1-4; pg. 388, col. 2, para. 3, lines 1-5). This describes receiving a sample from the product of interest of seafood comprising genomic DNA.
Regarding the recited amplifying the at least one DNA unique identifier sequence within the genomic DNA from the biological material and sequencing the DNA unique identifier sequence, Nicolè et al. discloses amplifying and sequencing the DNA barcode regions within the genomic DNA from the seafood samples (pg. 388, col. 2, para. 3, lines 1-6; pg. 389, col. 2, para. 1, lines 1-4). This describes amplifying and sequencing at least one identifier sequence.
Nicolè et al. and Barcaccia et al. do not disclose searching for the DNA unique identifier sequence in a database and retrieving a database entry corresponding with the DNA unique identifier sequence, the database entry providing identification and/or tracking information for the product of interest, wherein the identification and/or tracking information of the database entry comprises supply chain information for the product of interest.
However, Stoeckle et al. discloses recovering rbcL and matK barcodes from tea products, obtaining readable sequences from those barcodes, performing BLAST search through GenBank and Barcode of Life databases, and recording closest matches in each database (pg. 2, col. 1-2, para. 3, lines 1-12). This suggests conducting a BLAST search for the identifier sequence in a database and retrieving the corresponding database entry providing identification for the biological material. Also, further discloses barcode identifications associated with listed ingredients (pg. 3, col. 1, para. 2, lines 1-3; pg. 4, Table 1). This depicts supply chain information, including product and ingredient labels.
Claims 4 and 5 are rejected under 35 U.S.C. 103 as being unpatentable over Nicolè et al. (Food Technology and Biotechnology, 2012, 50(4), 387-398), Barcaccia et al. (Diversity, 2016, 8(1), 1-16), and Stoeckle et al. (Scientific Reports, 2011, 42(1), 1-7) as applied to claims 3, 8, 10, 12, 15, 52, and 56 above, in view of Roy et al. (Nature Biotechnology, 2018, 36, 512-520).
Nicolè et al., Barcaccia et al., and Stoeckle et al. are applied to claims 3, 8, 10, 12, 15, 52, and 56 above.
With respect to claim 4:
Nicolè et al., Barcaccia et al., and Stoeckle et al. do not disclose inserting at least one DNA unique identifier sequence within the genomic DNA of a biological entity, or modifying a pre-existing identifier sequence within the genomic DNA of a biological entity by gene editing to create a DNA unique identifier sequence within the genomic DNA of the biological entity, thereby providing identification thereof.
However, Roy et al. discloses a CRISPR-Cas9-based method for multiplexed accurate genome editing with short, trackable, integrated cellular barcodes (MAGESTIC) in Saccharomyces cerevisiae, which features genomic barcode integration (pg. 512, Abstract, lines 2-5). This suggests inserting an identifier sequence within the genomic DNA of a biological entity using MAGESTIC.
With respect to claim 5:
Nicolè et al., Barcaccia et al., and Stoeckle et al. do not disclose providing the at least one DNA unique identifier sequence for the insertion within the genomic DNA of the biological entity.
However, Roy et al. discloses using paired-end sequencing to assign barcodes to their corresponding guide-donor sequence (pg. 513, col. 1, para. 1, lines 8-10, Fig. 1a). This describes providing an identifier sequence for insertion.
It would have been prima facie obvious to one of ordinary skill in the art to modify the teachings disclosed by Nicolè et al., Barcaccia et al., and Stoeckle et al. to incorporate inserting an identifier sequence into genomic DNA using gene editing disclosed by Roy et al. One would be motivated to insert the identifier sequence by gene editing because MAGESTIC efficiently integrates the plasmid barcode into the genome and removes residual guide, which allows for downstream validation of individual variants from a mutant pool (pg. 518, col. 2, para. 2, lines 16-26). This means that the gene editing method disclosed by Roy et al. would be very efficient in inserting the identifier sequence for the method of traceability disclosed by Nicolè et al., Barcaccia et al., and Stoeckle et al. There is a likelihood of success, since both DNA barcoding and gene editing are well known techniques in the field of molecular biology.
Claims 11 and 60 are rejected under 35 U.S.C. 103 as being unpatentable over Nicolè et al. (Food Technology and Biotechnology, 2012, 50(4), 387-398), Barcaccia et al. (Diversity, 2016, 8(1), 1-16), and Stoeckle et al. (Scientific Reports, 2011, 42(1), 1-7) as applied to claims 3, 8, 10, 12, 15, 52, and 56 above, in view of Gibson et al. (Science, 2008, 319(5867), 1215-1220).
Nicolè et al., Barcaccia et al., and Stoeckle et al. are applied to claims 3, 8, 10, 12, 15, 52, and 56 above.
With respect to claim 11:
Nicolè et al., Barcaccia et al., and Stoeckle et al. do not disclose wherein the DNA unique identifier sequence comprises a unique nucleotide sequence inserted into an intergenic region of the genomic DNA.
However, Gibson et al. discloses DNA watermarks, sequences used to identify or encode information into DNA, which are inserted into intergenic sites of the genome (pg. 1215, col. 3, para. 2, lines 2-15). This describes an identifier sequence inserted into an intergenic region of the genomic DNA.
With respect to claim 60:
Nicolè et al., Barcaccia et al., and Stoeckle et al. do not disclose wherein one or more DNA unique identifier is present in one more innocuous site in the genome of the biological entity.
However, Gibson et al. discloses DNA watermarks, sequences used to identify or encode information into DNA, which are inserted into intergenic sites of the genome (pg. 1215, col. 3, para. 2, lines 2-15). This suggests that an identifier sequence is present in an innocuous site because some intergenic sites may be innocuous.
It would have been prima facie obvious to one of ordinary skill in the art to modify the teachings disclosed by Nicolè et al., Barcaccia et al., and Stoeckle et al. to incorporate the identifier sequence located at an innocuous site disclosed by Gibson et al. One would be motivated to insert the identifier sequence at an innocuous site because the watermark sequences disclosed by Gibson et al. are located at sites such that it is expected to have minimal biological effects and allow for easy differentiation between the synthetic genome and the native genome (pg. 1215, col. 3, para. 2, lines 11-15). This means that inserting the identifier sequence at an innocuous site will have fewer biological effects on the biological entity. There is a likelihood of success, since both DNA barcoding and watermark sequences as part of the genome assembly process are similar techniques well known in the field of molecular biology.
Claim 19 is rejected under 35 U.S.C. 103 as being unpatentable over Nicolè et al. (Food Technology and Biotechnology, 2012, 50(4), 387-398), Barcaccia et al. (Diversity, 2016, 8(1), 1-16), and Stoeckle et al. (Scientific Reports, 2011, 42(1), 1-7) as applied to claims 3, 8, 10, 12, 15, 52, and 56 above, in view of Tabler et al. (Nucleic Acids Research, 1996, 24(17), 3437-3438).
Nicolè et al., Barcaccia et al., and Stoeckle et al. are applied to claims 3, 8, 10, 12, 15, 52, and 56 above.
With respect to claim 19:
Nicolè et al. and Barcaccia et al. do not disclose wherein the DNA unique identifier sequence is a random sequence derived from a randomized pool of nucleic acid sequences of up to about 1500nt in length; up to about 1000nt in length; about 200nt to about 600nt in length; about 200nt to about 400nt in length; or about 400nt to about 600nt in length.
However, Stoeckle et al. discloses that the rbcL and matK barcode sequences are about 550 bp and 790 bp, respectively (pg. 1, para. 4, lines 1-3). Because rbcL and matK genes are double-stranded, converting from base pairs to number of nucleotides in length gives
550
x
2
=
1100
nt and
790
x
2
=
1580
nt, respectively.
Tabler et al. discloses from a library of nucleic acid molecules, which are randomized in parts of their sequence, unique sequence variants can be selected for specific properties (pg. 3437, Abstract, lines 1-4). This suggests selecting a unique DNA sequence from a pool of randomized DNA sequences.
It would have been prima facie obvious to one of ordinary skill in the art to combine the teachings disclosed by Nicolè et al., Barcaccia et al., and Stoeckle et al. with the selection of a DNA sequence from a library of random DNA sequences disclosed by Tabler et al. One would be motivated to combine the teachings with the randomized pool of DNA sequences because each further increase of the pool size by a factor of 2.3 (-ln10) will reduce the number of unrepresented sequences by a factor of 10. (pg. 3437, col. 1, para. 2, lines 1-6). This means that the larger the randomized pool of nucleic acid sequences, the better the selection of sequence as all sequences are represented. There is a likelihood of success, since both DNA barcoding and randomized pools of nucleic acid sequences are well known elements in the field of molecular biology.
Claim 28 is rejected under 35 U.S.C. 103 as being unpatentable over Nicolè et al. (Food Technology and Biotechnology, 2012, 50(4), 387-398), Barcaccia et al. (Diversity, 2016, 8(1), 1-16), and Stoeckle et al. (Scientific Reports, 2011, 42(1), 1-7) as applied to claims 3, 8, 10, 12, 15, 52, and 56 above, in view of Meiklejohn et al. (PLoS One, 2019, 14(6), 1-14) and Cold Spring Harbor Laboratory DNA Learning Center (DNA Barcoding 101, 2014 1-42).
Nicolè et al., Barcaccia et al., and Stoeckle et al. are applied to claims 3, 8, 10, 12, 15, 52, and 56 above.
With respect to claim 28:
Barcaccia et al. and Stoeckle et al. do not disclose receiving at a computing device the DNA-unique identifier sequence (DUID) extracted from a known biological material.
However, Nicolè et al. discloses extracting genomic DNA from seafood-derived specimens and generated amplification products from them, which are subsequently deposited in the NCBI database (pg. 390, col. 2, para. 1). This suggests receiving identifier sequences extracted from known biological material.
Barcaccia et al. and Stoeckle et al. do not disclose searching at the computing device a DUID database storing a plurality of DUIDs in association with respective biological material information for a match to the received DUID.
However, Nicolè et al. discloses conducting a similarity analysis and a phylogenetic approach to compare amplified sequences to reference sequences in the GenBank and BOLD databases (pg. 390, col. 1, para. 2, lines 1-4; pg. 390, col. 1, para. 3, lines 1-4). This suggests searching through databases of identifier sequences for a match to the amplified sequences.
Nicolè et al., Barcaccia et al., and Stoeckle et al. do not disclose if the search of the DUID database fails to provide a match to the received DUID, storing in the DUID database the received DUID in association with biological material information associated with the known biological material.
However, Cold Spring Harbor Laboratory DNA Learning Center discloses sequencing results are used to search a DNA database and if the barcode sequence is new, identification may rely on placing the unknown species in a phylogenetic tree with near relatives and the barcode can be submitted to GenBank (pg. 4, para. 2). This suggests that if there is no match for the received identifier sequence, store it in the database along with its biological material information.
Nicolè et al., Barcaccia et al., Stoeckle et al., and Cold Spring Harbor Laboratory DNA Learning Center do not disclose subsequent to storing the received DUID and with information associated with the known biological material in the DUID database, receiving at the computing device a query DUID extracted from an unknown biological material.
However, Meiklejohn et al. discloses searching an unknown barcode sequence against GenBank (pg. 10, para. 4, lines 7-11). This suggests receiving a query identifier sequence extracted from an unknown biological material.
Nicolè et al., Barcaccia et al., Stoeckle et al., and Cold Spring Harbor Laboratory DNA Learning Center do not disclose searching at the computing device the DUID database for a match to the received query DUID.
However, Meiklejohn et al. discloses searching an unknown barcode sequence against GenBank and using percent similarity to determine the confidence of a match (pg. 10, para. 4, lines 7-15). This suggests searching a database for a match to the received identifier sequence.
Nicolè et al., Barcaccia et al., Stoeckle et al., and Cold Spring Harbor Laboratory DNA Learning Center do not disclose if the search of the DUID provides a match to the received query DUID, returning in response to the received query DUID the biological information stored in association with the DUID matching the query DUID.
However, Meiklejohn et al. discloses searching unknown barcode sequences against GenBank and comparing the outputs from the searches with respect to the genus and species level classifications, ambiguous matches, or top match statistics (pg. 10, para. 4, lines 7-15). This suggests that if the search for the identifier sequence provides a match, results including biological information such as genus and species level classifications are outputted.
It would have been prima facie obvious to one of ordinary skill in the art to modify the teachings disclosed by Nicolè et al., Barcaccia et al., and Stoeckle et al., incorporate storing new identifier sequences disclosed by Cold Spring Harbor Laboratory DNA Learning Center and searching for identifier sequences from unknown biological material disclosed by Meiklejohn et al. One would be motivated to incorporate storing new identifier sequences because DNA barcoding, disclosed by Cold Spring Harbor Laboratory DNA Learning Center, was able to revolutionize the classification of orchids and catalogue many species of bees and butterflies in community gardens in New York City, identifying an urban environment as diverse (pg. 4, para. 3). Therefore, storing new identifier sequences in the method of DNA barcoding disclosed by Nicolè et al., Barcaccia et al., and Stoeckle et al. is significant in providing insight on biological diversity. Meiklejohn et al. also discloses that one main advantage of DNA barcoding is that extensive public reference databases of barcode sequences already exist; an unknown sequence can easily be searched against a database to determine the closest species match (pg. 2, para. 1, lines 11-14). This suggests that DNA barcoding is capable of searching identifier sequences associated with unknown biological material with ease. There is a likelihood of success, since these are all methods of DNA barcoding and are well known in the field of molecular biology.
Claim 29 is rejected under 35 U.S.C. 103 as being unpatentable over Nicolè et al. (Food Technology and Biotechnology, 2012, 50(4), 387-398), Barcaccia et al. (Diversity, 2016, 8(1), 1-16), Stoeckle et al. (Scientific Reports, 2011, 42(1), 1-7), Meiklejohn et al. (PLoS One, 2019, 14(6), 1-14), and Cold Spring Harbor Laboratory DNA Learning Center (DNA Barcoding 101, 2018, 1-42) as applied to claims 3, 8, 10, 12, 15, 28, 52, and 56 above, in view of McGinnis et al. (Nucleic Acids Research, 2004, 32, W20-W25).
Nicolè et al., Barcaccia et al., Stoeckle et al., Meiklejohn et al., and Cold Spring Harbor Laboratory DNA Learning Center are applied to claims 3, 8, 10, 12, 15, 28, 52, and 56 above.
With respect to claim 29:
Barcaccia et al., Stoeckle et al., Meiklejohn et al., and Cold Spring Harbor Laboratory DNA Learning Center do not disclose wherein searching the DUID database for a match to the received DUID or the query DUID.
However, Nicolè et al. discloses conducting a similarity analysis and a phylogenetic approach to compare amplified sequences to reference sequences in the GenBank and BOLD databases (pg. 390, col. 1, para. 2, lines 1-4; pg. 390, col. 1, para. 3, lines 1-4). This suggests searching through databases of identifier sequences for a match to the amplified sequences.
Barcaccia et al., Stoeckle et al., Meiklejohn et al., and Cold Spring Harbor Laboratory DNA Learning Center do not disclose searching the DUID database for an exact match to the received DUID.
However, Nicolè et al. discloses conducting a similarity analysis and a phylogenetic approach to compare amplified sequences to reference sequences in the GenBank and BOLD databases (pg. 390, col. 1, para. 2, lines 1-4; pg. 390, col. 1, para. 3, lines 1-4). This suggests searching the databases for a match to the amplified sequences.
Nicolè et al., Barcaccia et al., Stoeckle et al., Meiklejohn et al., and Cold Spring Harbor Laboratory DNA Learning Center do not disclose or if the search provides a close match to the query DUID, storing the query DUID in association with the DUID that is a close match to the query DUID.
However, McGinnis et al. discloses that when a query sequence is submitted, the search is sent to the BLAST server and a ‘Request Identifier’ (RID) is returned. The query and results are stored in a structured format for up to 24 hours after an RID is issued (pg. W20, col. 2, para. 2, lines 1-10). This suggests that if the search provides a match to the query sequence, storing the query sequence in association with the match results.
It would have been prima facie obvious to one of ordinary skill in the art to modify the teachings disclosed by Nicolè et al., Barcaccia et al., Stoeckle et al., Meiklejohn et al., and Cold Spring Harbor Laboratory DNA Learning Center to incorporate storing a query identifier sequence after searching for a match as disclosed by McGinnis et al. One would be motivated to modify the teachings so that this BLAST aspect is implemented because the Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program that finds short matches between two sequences and provides statistical information to help decipher biological significance of alignments (pg. W20, col. 1, para. 1). This is a known software used to perform sequence analysis, which is applicable to a known method for providing traceability of biological material disclosed by Nicolè et al., Barcaccia et al., Stoeckle et al., Meiklejohn et al., and Cold Spring Harbor Laboratory DNA Learning Center. There is a likelihood of success, since both the method and alignment tool are commonly used together to determine traceability of biological material and are well known in the field of molecular biology before the effective filing date of the claimed invention.
Claim 61 is rejected under 35 U.S.C. 103 as being unpatentable over Nicolè et al. (Food Technology and Biotechnology, 2012, 50(4), 387-398), Barcaccia et al. (Diversity, 2016, 8(1), 1-16), Stoeckle et al. (Scientific Reports, 2011, 42(1), 1-7), and Gibson et al. (Science, 2008, 319(5867), 1215-1220) as applied to claims 3, 8, 10, 12, 15, 52, 56, and 60 above, in view of Jupiter et al. (PLoS Pathogens, 2010, 6(6), 1-3).
Nicolè et al., Barcaccia et al., Stoeckle et al., and Gibson et al. are applied to claims 3, 8, 10, 12, 15, 52, 56, and 60 above.
With respect to claim 61:
Nicolè et al., Barcaccia et al., Stoeckle et al., and Gibson et al. do not disclose wherein the one or more DNA unique identifier at the one or more innocuous site does not affect gene expression or phenotype of the biological entity.
However, Jupiter et al. discloses previous studies have suggested that appropriately placed DNA watermarks can be phenotypically neutral (pg. 1, col. 3, para. 1, lines 9-12). This implies an identifier sequence at an innocuous site that does not affect the phenotype of a biological entity.
It would have been prima facie obvious to one of ordinary skill in the art to modify the teachings disclosed by Nicolè et al., Barcaccia et al., Stoeckle et al., and Gibson et al. to incorporate the DNA watermark disclosed by Jupiter et al. One would be motivated to modify the teachings so that the DNA identifier sequence does not affect the phenotype of the biological entity because the development and implementation costs for the proposed watermark implementation strategy disclosed by Jupiter et al. may prove to be much less than other proposed measures for enhancing laboratory security (pg. 3, col. 1-2, para. 1, lines 14-18). This means that it would be less costly to implement a DNA identifier sequence that does not affect the biological entity. There is a likelihood of success, since DNA barcoding and DNA watermarking are similar techniques well known in the field of molecular biology.
Conclusion
No claims are allowed.
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/J.N.L./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686
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