Remarks
Claims 1-10, 21, and 22 are pending.
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 .
Continued Examination Under 37 CFR 1.114
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 examination 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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 on 10/22/2025 has been entered.
Response to Arguments
Applicant's arguments filed 10/22/2025 have been fully considered but they are not persuasive.
Applicant appears to rely on the amended language “the digital watermark is usable to identify unauthorized use or distribution of the genomic data file or to verify the genomic data file” with respect to the 101 rejection. However, the claim does not include any step of identifying unauthorized use/distribution or verifying the file. Thus, this cannot be relied upon for overcoming an abstract idea based rejection. Please also see the 112 rejections below.
Applicant alleges that “a human cannot apply a digital watermark to at least a portion of a genomic data file storing genomic data using pen and paper.” To the contrary, as noted by Merriam Webster, (e.g., https://www.merriam-webster.com/dictionary/digital), the definition of “digital” includes “done with a finger”, which is precisely a human doing something with pen and paper. As explained previously and below, a human can, in fact perform the previous claims and current claims with pen and paper. For example, taking a genomic data file of some kind (e.g., a listing of genomic variation data), a human could watermark such by generating a first random seed using a secret key (e.g., performing a one way function, such as XOR, between a secret key and another piece of data”, generating a set of integers using the seed, for example, by writing them down, or by converting from binary to decimal, as examples, generating a second seed using dynamic attribute information by performing any function on any attribute data, such as by adding a certain amount to each attribute, selecting watermark positions in the integers by selecting positions corresponding to “1” in the second seed, modifying data by adding or subtracting, and transmitting by placing the paper in an envelope and handing it to another person or putting it another person’s mailbox. Therefore, the entirety of claim 1 can be performed by a human using pen and paper.
Applicant then appears to argue that every limitation in claim 1 is directed to additional elements. Please see the rejection below, which fully details anything that may be an additional element. The rest of this paragraph (the first paragraph on page 8 of the response), appears to simply be general allegations and/or are directed to non-claimed subject matter (e.g., “pp. 7-10 of the subject application”). Please see the below rejections.
With respect to the previous 112 rejection, Applicant fails to identify just how the entity being sent the file has anything to do with the “method of dynamically applying a digital watermark to at least a portion of a genomic data file storing genomic data”. No reception of anything is claimed, and the entity to which the file is transmitted has no effect on the scope of the claim. Despite Applicant’s belief that “claim 21 affects the scope of corresponding independent claim 1 … specifically the claim 1 element of ‘transmitting the watermarked file to an entity,’ by specifying that the transmission is to an entity that satisfies the dynamic attribute information”, claim 1 works the same exact way no matter who the entity is.
If Applicant were to amend positive steps that occur during watermark applying, then this may work. For example:
Reading a policy from storage;
Reading the name of an entity from the storage;
Comparing the name to the policy;
Determining that the name is in the policy;
Based on determining that the name is in the policy, determining that the entity satisfies the dynamic attribute information; and
Transmitting the watermarked file to the entity.
Disclaimer: The application as originally filed has not been reviewed for any particular subject matter that could be added; the above is simply a hypothetical example, and is not intended for use in the claims.
However, as of now, claim 21 simply defines data and the entity, without any actual positive step occurring in the method applying a watermark, as in claim 1.
Applicant alleges “the Action did not provide any response to the argument that Vlachos (even when combined with Ghose) fails to select (and modify data at) watermark positions in the manner recited in claim 1.” However, Applicant fails to identify just which argument Applicant believes the office action did not respond to. In fact, the office action responded to every argument to the extent required by each given argument. Thus, Applicant’s argument is, itself, in error.
With respect to Applicant’s allegations in the paragraph spanning pages 10-11, the generation of the second random seed is found in Vlachos’ disclosure of a seed or other random/pseudorandom value being generated from attribute information of any kind, such as the watermark, key, key portion, hash, etc., as examples. In this paragraph, Applicant alleges “Vlachos does not teach that the selected locations for watermark embedding, selected starting locations, etc. described in paragraphs 44-49 (which relate to fragile watermarking, as noted above) are selected by selecting, using a second random set, a subset of the locations for inserting the robust watermark (relied upon in the Action to allegedly teach the ordered pseudorandom set of integers, as noted above).” However, Applicant fails to tie this to the claim limitations Applicant is attempting to argue. It appears as though Applicant is arguing that the claim requires selecting locations by selecting, using a second random set, a subset of the locations for inserting the … watermark. However, this is not required by claim 1. In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., selecting, using a second random set, a subset of the locations for inserting the … watermark) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
Claim 1 does call for “selecting watermark positions in the genomic data file by selecting, using the second random seed, a subset of the ordered pseudorandom set of integers, the subset corresponding to identifiers of data locations in the genomic data file”, which is met by Vlachos as modified by Ghose as follows:
Vlachos discloses …
…
Selecting watermark positions in the data file by selecting, using the second random seed, a subset of the ordered pseudorandom set of integers, the subset corresponding to identifiers of data locations in the data file (Exemplary Citations: for example, Paragraphs 33, 44-49 and associated figures; selecting locations for watermark embedding, selecting starting locations, selecting signal blocks, choosing which values are modified by +1 or -1 (but 0’s are not modified, thus not being selected), etc., as examples);
…
Ghose, however, discloses that the data file is a genomic data file (Exemplary Citations: for example, Paragraphs 8-12, 22, 23, 25-29, 33, 34, and associated figures; watermarking allele frequencies and/or any data associated with variants in VCF file or list of variants, for example. Applicant has also stated, for example, on page 8 of the response dated 2/20/2025, that Ghose discloses “the watermark generator is applied after a graph builder that builds a graph from a list of variants in VCF format to generate a watermarked reference graph”, thus clearly showing watermarking a genomic data file including a graph build from variants, for example). …
With respect to the first full paragraph on page 11 of the response, Vlachos clearly discloses selecting watermark positions in the data file by selecting, using the second random seed, a subset of the ordered pseudorandom set of integers, the subset corresponding to identifiers of data locations in the data file in Vlachos’ disclosure of selecting locations for watermark embedding, such as for the fragile watermark, which may involve selecting starting locations, selecting blocks/segments, and the like. It is noted that these may be select this using random seeds, such as paragraph 48 seeding a PRNG to generate “randomly located intervals” for insertion of the fragile watermark. Paragraph 48 also discusses using “the embedded metadata as the seed of a random number generator to generate the final fragile watermark containing zeros and ones of length equal to the duration of a given block”, thus showing that the selection of locations (e.g., in one example, the locations of the 1’s) is based off the robust watermark which may include at least the embedded metadata. Thus, random seeds are certainly used to select positions in the file for watermarking.
Applicant then alleges “As Ghose provides no disclosure of selecting watermark positions using as seed…”. However, Applicant fails to support this general allegation with any actual argument. Applicant's arguments fail to comply with 37 CFR 1.111(b) because they amount to a general allegation that the claims define a patentable invention without specifically pointing out how the language of the claims patentably distinguishes them from the references.
With respect to Applicant’s allegations in the paragraph spanning pages 11-12 of the response, it is noted that claim 3 does not require a VCF file, but rather, includes a Markush group, where the genomic data file could be either a VCF file or a list of variants storing genomic variation data. As noted by Applicant, as shown in FIG. 4 of Ghose, the watermark generator is applied after a graph builder builds a graph from a list of variants in VCF format to generate a watermarked reference graph”. This graph itself is a list of variants, since it is built from the VCF file and includes multiple values listed in graph format. For example, paragraph 33 states “A graph builder 210 receives a genomic sequence including a list of variants 215 occurring in natural DNA, and creates a graph representation thereof e.g., a directed acyclic graph including multiple paths reflecting the different variants”, showing a listing of variants in the paths, for example. The claims do not require a VCF file being directly watermarked, rather, any listing of variants suffices, such as the graph of Ghose.
With respect to Applicant’s general allegation regarding claim 22, Applicant is directed to the below rejection of this new subject matter. As noted below, Vlachos as modified by Ghose discloses that modifying the data in the selected data locations of the genomic data file comprises replacing a reference base determined by a sequence read at respective selected data locations of the genomic data with a respective selected alternate genomic base in the combination’s disclosure of watermarking any base as in Vlachos, as well as genomic bases as in Ghose, for example.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-10, 21, and 22 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 1 states “modifying data at selected data locations in the data file corresponding to at least a portion of the identifiers included in the subset to generate a watermarked file with the digital watermark, wherein the digital watermark is perceptible after applying an algorithm and usable to identify unauthorized use or distribution of the genomic data file or to verify the genomic data file”. However, the application as originally filed does not disclose, as part of the step of “modifying data at selected data locations in the data file corresponding to at least a portion of the identifiers included in the subset to generate a watermarked file with the digital watermark”, somehow having the digital watermark become perceptible after applying an algorithm and usable to identify unauthorized use or distribution of the genomic data file or to verify the genomic data file”. In fact, the application as originally filed discloses that the watermark can only be verified after the file is modified. Claims 2-10, 21, and 22 are rejected at least based on their dependencies.
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 1-10, 21, and 22 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.
Claim 1 states “modifying data at selected data locations in the data file corresponding to at least a portion of the identifiers included in the subset to generate a watermarked file with the digital watermark, wherein the digital watermark is perceptible after applying an algorithm and usable to identify unauthorized use or distribution of the genomic data file or to verify the genomic data file”. However, it is unclear just how the step of “modifying data at selected data locations in the data file corresponding to at least a portion of the identifiers included in the subset to generate a watermarked file with the digital watermark” can include having the digital watermark become perceptible after applying an algorithm and usable to identify unauthorized use or distribution of the genomic data file or to verify the genomic data file”. The whole point of watermarks is that they are used for verification later on, after the watermarked file is created, not during creation of the watermarked file. As noted above, the application as originally filed does not have basis for this either. Claims 2-10, 21, and 22 are rejected at least based on their dependencies.
Claim 21 states “wherein the entity to which the watermarked file is transmitted satisfies the dynamic attribute information”. However, the claim is not directed to this entity, so it is unclear just how the method of claim 1 is ensuring that the entity satisfies the dynamic attribute information. It is also unclear just how an entity can go about satisfying the dynamic attribute information. Moreover, it is unclear how the entity to which something is being transmitted can possibly affect the scope of a method for applying a watermark to a file.
Claim Rejections - 35 USC § 101
Claims 1-10, 21, and 22 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Regarding claim 1, with respect to step 1, this part of the eligibility analysis evaluates whether the claim falls within any statutory category. MPEP 2106.03. The claim recites a method of dynamically applying a digital watermark to at least a portion of a genomic data file storing genomic data, the method comprising: generating, using information derived from a secret key, a first random seed; generating, using the first random seed, an ordered pseudorandom set of integers; generating, using dynamic attribute information, a second random seed; selecting watermark positions in the genomic data file by selecting, using the second random seed, a subset of the ordered pseudorandom set of integers, the subset corresponding to identifiers of data locations in the genomic data file; modifying data at selected data locations in the genomic data file corresponding to at least a portion of the identifiers included in the subset to generate a watermarked file with the digital watermark, wherein the digital watermark is perceptible after applying an algorithm and usable to identify unauthorized use or distribution of the genomic data file or to verify the genomic data file; and transmitting the watermarked file to an entity. Therefore, this claim appears to be a method, which is a statutory category of invention. Please see MPEP 2106.3.I:
A process defines "actions", i.e., an invention that is claimed as an act or step, or a series of acts or steps. As explained by the Supreme Court, a "process" is "a mode of treatment of certain materials to produce a given result. It is an act, or a series of acts, performed upon the subject-matter to be transformed and reduced to a different state or thing." Gottschalk v. Benson, 409 U.S. 63, 70, 175 USPQ 673, 676 (1972) (italics added) (quoting Cochrane v. Deener, 94 U.S. 780, 788, 24 L. Ed. 139, 141 (1876)). See also Nuijten, 500 F.3d at 1355, 84 USPQ2d at 1501 ("The Supreme Court and this court have consistently interpreted the statutory term ‘process’ to require action"); NTP, Inc. v. Research in Motion, Ltd., 418 F.3d 1282, 1316, 75 USPQ2d 1763, 1791 (Fed. Cir. 2005) ("[A] process is a series of acts.") (quoting Minton v. Natl. Ass’n. of Securities Dealers, 336 F.3d 1373, 1378, 67 USPQ2d 1614, 1681 (Fed. Cir. 2003)). As defined in 35 U.S.C. 100(b), the term "process" is synonymous with "method."
The other three categories (machines, manufactures and compositions of matter) define the types of physical or tangible "things" or "products" that Congress deemed appropriate to patent. Digitech Image Techs. v. Electronics for Imaging, 758 F.3d 1344, 1348, 111 USPQ2d 1717, 1719 (Fed. Cir. 2014) ("For all categories except process claims, the eligible subject matter must exist in some physical or tangible form."). Thus, when determining whether a claimed invention falls within one of these three categories, examiners should verify that the invention is to at least one of the following categories and is claimed in a physical or tangible form.
• A machine is a "concrete thing, consisting of parts, or of certain devices and combination of devices." Digitech, 758 F.3d at 1348-49, 111 USPQ2d at 1719 (quoting Burr v. Duryee, 68 U.S. 531, 570, 17 L. Ed. 650, 657 (1863)). This category "includes every mechanical device or combination of mechanical powers and devices to perform some function and produce a certain effect or result." Nuijten, 500 F.3d at 1355, 84 USPQ2d at 1501 (quoting Corning v. Burden, 56 U.S. 252, 267, 14 L. Ed. 683, 690 (1854)).
• A manufacture is "a tangible article that is given a new form, quality, property, or combination through man-made or artificial means." Digitech, 758 F.3d at 1349, 111 USPQ2d at 1719-20 (citing Diamond v. Chakrabarty, 447 U.S. 303, 308, 206 USPQ 193, 197 (1980)). As the courts have explained, manufactures are articles that result from the process of manufacturing, i.e., they were produced "from raw or prepared materials by giving to these materials new forms, qualities, properties, or combinations, whether by hand-labor or by machinery." Samsung Electronics Co. v. Apple Inc., 137 S. Ct. 429, 120 USPQ2d 1749, 1752-3 (2016) (quoting Diamond v. Chakrabarty, 447 U. S. 303, 308, 206 USPQ 193, 196-97 (1980)); Nuijten, 500 F.3d at 1356-57, 84 USPQ2d at 1502. Manufactures also include "the parts of a machine considered separately from the machine itself." Samsung Electronics, 137 S. Ct. at 435, 120 USPQ2d at 1753 (quoting 1 W. Robinson, The Law of Patents for Useful Inventions §183, p. 270 (1890)).
• A composition of matter is a "combination of two or more substances and includes all composite articles." Digitech, 758 F.3d at 1348-49, 111 USPQ2d at 1719 (citation omitted). This category includes all compositions of two or more substances and all composite articles, "'whether they be the results of chemical union or of mechanical mixture, or whether they be gases, fluids, powders or solids.'" Chakrabarty, 447 U.S. at 308, 206 USPQ at 197 (quoting Shell Dev. Co. v. Watson, 149 F. Supp. 279, 280 (D.D.C. 1957); id. at 310 holding genetically modified microorganism to be a manufacture or composition of matter).
With respect to step 2A, prong one, this part of the eligibility analysis evaluates whether the claim recites a judicial exception. As explained in MPEP 2106.04(II) and the October 2019 Update, a claim ‘recites’ a judicial exception when the judicial exception is ‘set forth’ or ‘described’ in the claim. There are no nature-based product limitations in the claim, and thus the markedly different characteristics analysis is not performed. However, the claim still must be reviewed to determine if it recites any other type of judicial exception.
Claim 1 recites the following limitations that are directed to abstract ideas:
A method of dynamically applying a digital watermark to at least a portion of a genomic data file storing genomic data, the method comprising (mental process and/or certain methods of organizing human activity, such as noted below, a human placing a watermark on a genomic data file, such as a piece of paper including any genomic data):
generating, using information derived from a secret key, a first random seed (e.g., mental process and/or certain methods of organizing human activity, such as pulling part of a random key or pulling random values from a key, or using a simple function (e.g., XOR) to randomize a key, etc.);
generating, using the first random seed, an ordered pseudorandom set of integers (e.g., mental process and/or certain methods of organizing human activity, this may be the seed itself, or any functions may be performed in the human mind or via pen and paper to create this set of integers);
generating, using dynamic attribute information, a second random seed (e.g., mental process and/or certain methods of organizing human activity, such as creating a random seed in any fashion, by randomly selecting numbers from some numerical attribute, by performing XOR, or the like, as examples);
selecting watermark positions in the genomic data file by selecting, using the second random seed, a subset of the ordered pseudorandom set of integers, the subset corresponding to identifiers of data locations in the genomic data file (e.g., mental process and/or certain methods of organizing human activity, using the second seed as an index to the integers, for example. Perhaps each number within the second seed is used as an offset from the previous location within the integers, as one simple example);
modifying data at selected data locations in the genomic data file corresponding to at least a portion of the identifiers included in the subset to generate a watermarked file with the digital watermark, wherein the digital watermark is perceptible after applying an algorithm and usable to identify unauthorized use or distribution of the genomic data file or to verify the genomic data file (e.g., mental process and/or certain methods of organizing human activity, erasing and re-writing values, adding marks to values, or any other modification that can be perceived once someone that knows how it was watermarked receives and attempts to verify it); and
transmitting the watermarked file to an entity (e.g., mental process and/or certain methods of organizing human activity, getting this to any entity, such as creating a paper airplane and gliding it to another human in the same room, placing in an envelope and dropping it in the mailbox, or any of myriad additional methods of human powered transmitting).
As noted, these can be performed by a human either completely mentally or by using certain methods of organizing human activity, such as a human writing and reading via documentation or filing systems.
As explained in the MPEP and the October 2019 Update, situations like this where a series of steps recite judicial exceptions, examiners should combine all recited judicial exceptions and treat the claim as containing a single abstract idea for purposes of further eligibility. See MPEP 2106.04 and 2106.05(ii). Thus, for purposes of further discussion, this rejection may consider all limitations as a single abstract idea.
With respect to step 2A, prong two, this part of the eligibility analysis evaluates whether the claim as a whole integrates the recited judicial exception into a practical application of the exception. This evaluation is performed by (a) identifying whether there are any additional elements recited in the claim beyond the judicial exception, and (b) evaluating those additional elements individually and in combination to determine whether the claim as a whole integrates the exception into a practical application. 2019 PEG Section III(A)(2), 84 Fed. Reg. at 54-55. The independent claims also recite the following additional elements: there are no additional elements.
Even if Applicant were to amend the claims to require that the word “digital” is taken in the computer realm instead of the digits of one’s hand, this hypothetical additional element would be recited so generically (no details are provided other than that the watermark is digital) that it represents no more than mere instructions to apply the judicial exception on a computer system. This limitation can also be viewed as nothing more than an attempt to generally link the use of the judicial exception to the technological environment of a computer. It should be noted that because the courts have made clear that mere physicality or tangibility of an additional element or elements is not a relevant consideration in the eligibility analysis, the nature of these components being physical or tangible does not affect this analysis. See MPEP 2106.05(I) for more information on this point, including explanations from judicial decisions including Alice Corp. Pty. Ltd. V. CLS Bank Int’l, 573 U.S. 208, 224-26 (2014).
Even when viewed in combination, any additional elements in this claim do no more than automate the abstract ideas that the human can perform, using computer components as a tool. There is no improvement to any computers or other technology achieved by the claim by automating the abstract ideas, and thus this claim cannot improve computer functionality or other technology. See, e.g., Trading Technologies Int’l v. IBG, Inc., 921 F.3d 1084, 1093 (Fed. Cir. 2019) (using a computer to provide a trader with more information to facilitate market trades improved the business process of market trading, but not the computer) and the cases discussed in MPEP 2106.05(a)(I), particularly FairWarning IP, LLC v. Iatric Sys., 839 F.3d 1089, 1095 (Fed. Cir. 2016) (accelerating a process of analyzing audit log data is not an improvement when the increased speed comes solely from the capabilities of a general-purpose computer) and Credit Acceptance Corp. v. Westlake Services, 859 F.3d 1044, 1055 (Fed. Cir. 2017)(using a generic computer to automate a process of applying to finance a purchase is not an improvement to the computer’s functionality). Accordingly, the claim as a whole does not integrate the recited judicial exception into a practical application and the claim is directed to the judicial exception.
With respect to step 2B, this part of the eligibility analysis evaluates whether the claim as a whole amounts to significantly more than the recited exception, i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim. MPEP 2106.05. As explained with respect to Step 2A Prong Two, the additional element(s) described above is/are at best the equivalent of merely adding the words “apply it” to the judicial exception. Mere instructions to apply an exception cannot provide an inventive concept. Any other additional elements identified above are extra-solution activity, which for purposes of Step 2A Prong Two was considered insignificant. Under the 2019 PEG, however, a conclusion that an additional element is insignificant extra-solution activity in Step 2A should be re-evaluated in Step 2B. 2019 PEG Section III(B), 84 Fed. Reg. at 56. At Step 2B, the evaluation of the insignificant extra-solution activity consideration takes into account whether or not the extra-solution activity is well-known. See MPEP 2106.05(g). Here, any insignificant extra solution activity is within the examples provided in USPTO guidance, such as MPEP 2106.05(g), for example. Thus, any subject matter that may be considered extra-solution activity therefore remain insignificant extra-solution activity even upon reconsideration, and do not amount to significantly more. Even when considered in combination, these additional elements represent mere instructions to apply an exception and insignificant extra-solution activity, which cannot provide an inventive concept.
Claims 2-4 discuss data and do nothing to aid in overcoming any abstract idea(s).
Claim 5 includes some math, which appears to be possible for a human to perform, having the same analysis as claim 1 above.
Claims 6 and 7 discuss how N is selected, which is within the abilities of a human, having the same analysis as claim 1 above.
Claims 8 and 9 include hash functions, which have a similar analysis as above, since a simple hash function (e.g., XOR and truncate) is within the abilities of a human.
Claim 10 includes encrypting, which is certainly within the abilities of a human and has the same analysis as above. It is noted that encryption has been around since long before computers. The Caeser Cipher is one rather old encryption technique that has been around for millennia.
Claim 21 discusses data and an entity, with does nothing in overcoming any abstract idea(s).
Claim 22 may be met by a human erasing a genomic base that appears on the paper initially and replacing it with another genomic base, having the same analysis as claim 1 above.
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.
Claims 1-4, 21, and 22 are rejected under 35 U.S.C. 103 as being unpatentable over Vlachos (U.S. Patent Application Publication 2009/0226056) in view of Ghose (U.S. Patent Application Publication 2018/0253536).
Regarding Claim 1,
Vlachos discloses a method of dynamically applying a digital watermark to at least a portion of a data file storing genomic data, the method comprising:
Generating, using information derived from a secret key, a first random seed (Exemplary Citations: for example, Paragraphs 11, 21-25, 30-32, and associated figures; any seed, such as frequencies, watermark values once generated with secret key, etc., as examples);
Generating, using the first random seed, an ordered pseudorandom set of integers (Exemplary Citations: for example, Paragraphs 11, 21-25, 30-32, and associated figures; locations for watermark/robust watermark, modified values, modifications, etc., as examples);
Generating, using dynamic attribute information, a second random seed (Exemplary Citations: for example, Paragraphs 44-49 and associated figures; seed or other random/pseudorandom value being generated from attribute information of any kind, such as the watermark, key, key portion, hash, etc., as examples);
Selecting watermark positions in the data file by selecting, using the second random seed, a subset of the ordered pseudorandom set of integers, the subset corresponding to identifiers of data locations in the data file (Exemplary Citations: for example, Paragraphs 33, 44-49 and associated figures; selecting locations for watermark embedding, selecting starting locations, selecting signal blocks, choosing which values are modified by +1 or -1 (but 0’s are not modified, thus not being selected), etc., as examples);
Modifying data at selected data locations in the data file corresponding to at least a portion of the identifiers included in the subset to generate a watermarked file with the digital watermark, wherein the digital watermark is perceptible after applying an algorithm and usable to identify unauthorized use or distribution of the genomic data file or to verify the genomic data file (Exemplary Citations: for example, Paragraphs 11, 21-25, 30-33, 44-49 and associated figures; watermarking the file, for example, and, although not claimed as a positive step, decoding and verifying the watermark, as discussed in the cited portions above as well as additional portions of Vlachos, such as paragraphs 38-43, 50, and associated figures); and
Transmitting the watermarked file to an entity (Exemplary Citations: for example, Paragraphs 7, 8, 20, 30, 39, 42, and associated figures; transmission and receipt of watermarked data over a channel, for example);
But does not explicitly disclose that the data file is a genomic data file.
Ghose, however, discloses that the data file is a genomic data file (Exemplary Citations: for example, Paragraphs 8-12, 22, 23, 25-29, 33, 34, and associated figures; watermarking allele frequencies and/or any data associated with variants in VCF file or list of variants, for example. Applicant has also stated, for example, on page 8 of the response dated 2/20/2025, that Ghose discloses “the watermark generator is applied after a graph builder that builds a graph from a list of variants in VCF format to generate a watermarked reference graph”, thus clearly showing watermarking a genomic data file including a graph build from variants, for example). It would have been obvious to one of ordinary skill in the art at the time of applicant’s invention, which is before any effective filing date of the claimed invention, to incorporate the watermarking in bioinformatic sequence analysis techniques of Ghose into the metadata embedding in medical data system of Vlachos in order to allow for additional data that can be watermarked, to provide security in additional formats and files, to allow for additional watermarking techniques, and/or to increase security in the system.
Regarding Claim 2,
Vlachos as modified by Ghose discloses the method of claim 1, in addition, Vlachos discloses that the dynamic attribute information includes entity information for an entity to which the file is being distributed to or shared with, timing information corresponding to a validity time period for accessing the file, a data usage policy for the file, and/or one or more other attributes of a policy for the data (Exemplary Citations: for example, Paragraphs 11, 21-25, 30-33, 44-49 and associated figures; any attribute, such as SSN, hash, ECC, etc., as examples).
Regarding Claim 3,
Vlachos as modified by Ghose discloses the method of claim 1, in addition, Ghose discloses that the genomic data file is a Variant Call Format (VCF) file or a list of variants storing genomic variation data, and wherein the watermarks are embedded in variant allele frequency and/or other rational data associated with the variants (Exemplary Citations: for example, Paragraphs 8-12, 22, 23, 25-29, 33, 34, and associated figures; watermarking allele frequencies and/or any data associated with variants in VCF file or list of variants, for example).
Regarding Claim 4,
Vlachos as modified by Ghose discloses the method of claim 3, in addition, Ghose discloses that the variant allele frequency is included in the genomic variation data and/or wherein the variant allele frequency is calculated based on an alternative alleles count for the genomic variation data and a depth of coverage at a variant position or a count of reference alleles for the genomic variation data (Exemplary Citations: for example, Paragraphs 8-12, 22, 23, 25-29, 33, 34, and associated figures; variant allele frequency, for example).
Regarding Claim 21,
Vlachos as modified by Ghose discloses the method of claim 1, in addition, Vlachos discloses that the dynamic attribute information includes one or more attributes of a policy for the data, wherein the entity to which the watermarked file is transmitted satisfies the dynamic attribute information (Exemplary Citations: for example, Paragraphs 7, 8, 20, 23, 30, 38, 39, 42, and associated figures; owners can access own data, and/or party, such as a third party, is authorized by the owner to access the data, for example).
Regarding Claim 22,
Vlachos as modified by Ghose discloses the method of claim 1, in addition, Vlachos as modified by Ghose discloses that modifying the data in the selected data locations of the genomic data file comprises replacing a reference base determined by a sequence read at respective selected data locations of the genomic data with a respective selected alternate genomic base (Vlachos: Exemplary Citations: for example, Paragraphs 11, 21-25, 30-33, 44-49 and associated figures; Ghose: Exemplary Citations: for example, Paragraphs 8-12, 22, 23, 25-29, 33, 34, and associated figures; watermarking any base as in Vlachos, as well as genomic bases as in Ghose, for example).
Claims 5-7 are rejected under 35 U.S.C. 103 as being unpatentable over Vlachos in view of Ghose and Lanman (WO 2018/213498).
Regarding Claim 5,
Vlachos as modified by Ghose does not explicitly disclose dividing a range of the variant allele frequency into a plurality of bins of size 1/N and shifting the bins by a half-length of 1/(2N), where a first bin and a last bin are each of size 1/(2N), assigning adjacent bins to a respective different one of two quantizers, selecting, for each variant position in the genomic variation data, a target bin size and a target quantizer index based on the secret key, and for each variant in the genomic variation data having a depth of coverage above a threshold, adjusting an alternative allele count such that a corresponding allele frequency for the variant falls into a selected one of the plurality of bins corresponding to the selected target bin size and target quantizer index.
Lanman, however, discloses dividing a range of the variant allele frequency into a plurality of bins of size 1/N and shifting the bins by a half-length of 1/(2N), where a first bin and a last bin are each of size 1/(2N) (Exemplary Citations: for example, Paragraphs 14, 15, 29, 71-81, 87, 88, 189, 190, 210, 223, 234, 259, 300, and associated figures; binning, where each bin may include anywhere from 0.1% of the values to 99.9% of the values, when there are 2 bins, each bin is effectively a half-shifted single bin (i.e., N=1), to create 2 bins of half length, etc., as examples);
Assigning adjacent bins to a respective different one of two quantizers (Exemplary Citations: for example, Paragraphs 14, 15, 29, 71-81, 87, 88, 189, 190, 210, 223, 234, 259, 300, and associated figures; different mappings, e.g., somatic for a somatic bin and germline for germline bin);
Selecting, for each variant position in the genomic variation data, a target bin size and a target quantizer index based on the secret key (Exemplary Citations: for example, Paragraphs 14, 15, 29, 71-81, 87, 88, 189, 190, 210, 223, 234, 254, 259, 300, and associated figures; bin size and value, for example); and
For each variant in the genomic variation data having a depth of coverage above a threshold, adjusting an alternative allele count such that a corresponding allele frequency for the variant falls into a selected one of the plurality of bins corresponding to the selected target bin size and target quantizer index (Exemplary Citations: for example, Paragraphs 14, 15, 29, 71-81, 87, 88, 189, 190, 210, 223, 234, 254, 259, 300, and associated figures; adjusting bins and/or variants above a threshold, for example). It would have been obvious to one of ordinary skill in the art at the time of applicant’s invention, which is before any effective filing date of the claimed invention, to incorporate the genomic binning techniques of Lanman into the metadata embedding in medical data system of Vlachos as modified by Ghose in order to allow the system to identify the somatic origin of DNA, to allow for determining of somatic vs. germline variants, and/or to better find the germline origin of DNA.
Regarding Claim 6,
Vlachos as modified by Ghose and Lanman discloses the method of claim 5, in addition, Lanman discloses that N is set to an integer greater than one, to preserve variant genotypes (Exemplary Citations: for example, Paragraphs 14, 15, 29, 71-81, 87, 88, 189, 190, 210, 223, 234, 259, 300, and associated figures; multiple (e.g., 3) bins, for example).
Regarding Claim 7,
Vlachos as modified by Ghose and Lanman discloses the method of claim 5, in addition, Lanman discloses randomly (Vlachos: Exemplary Citations: for example, Paragraphs 11, 21-25, 30-33, 44-49 and associated figures; randomizing various values, for example) selecting N from a range of numbers, wherein minimum and maximum values of the range correspond to lowest and highest resolution of quantizers, respectively (Exemplary Citations: for example, Paragraphs 14, 15, 29, 71-81, 87, 88, 189, 190, 210, 223, 234, 259, 300, and associated figures; selecting number of bins, for example).
Claims 8 and 9 are rejected under 35 U.S.C. 103 as being unpatentable over Vlachos in view of Ghose and Daly (U.S. Patent Application Publication 2015/0039614).
Regarding Claim 8,
Vlachos as modified by Ghose does not explicitly disclose securely hashing variant tuples of the genomic variation data to generate a plurality of hash values.
Daly, however, discloses securely hashing variant tuples of the genomic variation data to generate a plurality of hash values (Exemplary Citations: for example, Paragraphs 71, 82, 111, and associated figures; creating hashed tuple from DNA/RNA sequence including gaps due to variants, for example). It would have been obvious to one of ordinary skill in the art at the time of applicant’s invention, which is before any effective filing date of the claimed invention, to incorporate the variant tuple hashing techniques of Daly into the metadata embedding in medical data system of Vlachos as modified by Ghose in order to organize the genomic variant data into an efficient format that facilitates searching and matching of undefined sequences with known sequences, to provide smaller, easier to compare, values, and/or to increase security in the system.
Regarding Claim 9,
Vlachos as modified by Ghose and Daly discloses the method of claim 8, in addition, Daly discloses storing the hash values in a binary file (Exemplary Citations: for example, Paragraphs 6, 71, 82, 111, and associated figures; storing the above in a database or the like, for example).
Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Vlachos in view of Ghose, Daly, and Molyneaux (WO 2017/153456).
Regarding Claim 10,
Vlachos as modified by Ghose and Daly discloses the method of claim 8 or 9, in addition, Daly discloses securely hashing the variant tuples (Exemplary Citations: for example, Paragraphs 6, 71, 82, 111, and associated figures);
But does not explicitly disclose encrypting genomic positions of the variant tuples.
Molyneuax, however, discloses encrypting genomic positions of the variant tuples prior to hashing (Exemplary Citations: pages 11-12, encryption section; encrypting positions, for example). It would have been obvious to one of ordinary skill in the art at the time of applicant’s invention, which is before any effective filing date of the claimed invention, to incorporate the encryption techniques of Molyneuax into the metadata embedding in medical data system of Vlachos as modified by Ghose and Daly in order to encrypt data, to prevent unauthorized entities from accessing the data, to provide fine grained privacy control by enabling partial genomic data retrieval while addressing leakage threats, and/or to increase security in the system.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jeffrey D Popham whose telephone number is (571)272-7215. The examiner can normally be reached Monday through Friday 9:00-5:30.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Jeffrey Nickerson can be reached at (469) 295-9235. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/Jeffrey D. Popham/Primary Examiner, Art Unit 2432