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 .
Status of Claims
Claims 1-36 are pending.
Claims 1-36 are rejected.
Claims 5, 7, 9, 11, 17, 20-21 are objected to.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Accordingly, the effective filing date of the claimed invention is 11 June 2021.
Information Disclosure Statement
The information disclosure statement(s) (IDS) submitted on 17 June 2025, 17 Dec. 2025, 05 Jan. 2025, and 17 Jan. 2023 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the list of cited references was considered in full by the examiner.
Drawings
The replacement drawing sheets filed 17 Aug. 2022 have been entered.
The drawings are objected to because:
Figures 1-3, 5, 8, 10, and 11 fail to comply with 37 CFR 1.84(u)(1), which states partial views intended to form one complete view, on one or several sheets, must be identified by the same number followed by a capital letter. For example, “FIG. 1A-B” should include separate labels “FIG. 1A” and “FIG. 1B” for the respective partial reviews. The other figures should be corrected similarly.
FIG. 6 and 7 include reference characters (1)-(10). Applicant’s specification at para. [0160] mentions steps 1-5 in reference to Figure 1, and thus 1-6 appear to designate separate steps corresponding separately to FIG. 1 versus 6-7, which fails to comply with 37 CFR 1.84(p)(4).
FIG. 6-7 includes reference characters (7)-(10) which are not mentioned in the description, and thus fail to comply with 37 CFR 1.84(p).
FIG. 8 includes reference character 11-12 which is not mentioned in the description, and thus fail to comply with 37 CFR 1.84(p).
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(4) because:
reference character “3” has been used to designate both HPO phenotypes in FIG. 6-7 and clinical notes in FIG. 8;
reference character “4” has been used to designate both sample metadata in FIG. 6-7 and HPO phenotype in FIG. 8;
reference character “10” has been used to designate both “Supervision, Manual Confirmation” in FIG. 6-7 and “Filtered Variants” in FIG. 8
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
References to Applicant’s specification are made with respect to the published version.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code at para. [0187]. 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.
Applicant is reminded of the proper content of an abstract of the disclosure.
A patent abstract is a concise statement of the technical disclosure of the patent and should include that which is new in the art to which the invention pertains. The abstract should not refer to purported merits or speculative applications of the invention and should not compare the invention with the prior art.
If the patent is of a basic nature, the entire technical disclosure may be new in the art, and the abstract should be directed to the entire disclosure. If the patent is in the nature of an improvement in an old apparatus, process, product, or composition, the abstract should include the technical disclosure of the improvement. The abstract should also mention by way of example any preferred modifications or alternatives.
Where applicable, the abstract should include the following: (1) if a machine or apparatus, its organization and operation; (2) if an article, its method of making; (3) if a chemical compound, its identity and use; (4) if a mixture, its ingredients; (5) if a process, the steps.
Extensive mechanical and design details of an apparatus should not be included in the abstract. The abstract should be in narrative form and generally limited to a single paragraph within the range of 50 to 150 words in length.
See MPEP § 608.01(b) for guidelines for the preparation of patent abstracts.
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
The abstract of the disclosure is objected to because:
The abstract contains phrases which can be implied, including “The present disclosure provides” at line 1.
The invention relates to a process, but does not describe any steps of the process, and instead only discusses the purported merits of the invention (e.g. “comprehensive, scalable solution that solves diagnostic…” and “the invention provides Genome-to-Treatment..”).
A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Claim Objections
Claims 5, 7, 9, 11, 17, 20-21 are objected to because of the following informalities:
Claim 5 recites “wherein genetic sequencing comprises…”, which should be amended to recite “wherein the genetic sequencing comprises…” to increase clarity and refer to the sequencing step of claim 1, from which claim 5 depends.
Claim 7 recites “wherein the sample is blood, dried blood spot…”, which should recite “…wherein the biological sample…” to use consistent language with claim 6 and increase clarity.
Claim 9 recites “…wherein determining genetic variants of (e)”, which should be amended to recite “…wherein determining the genetic variants of (e)” to increase clarity and use consistent language.
Claim 11 recites “…only genetic variants…is retained…” which is a grammatical error and should recite “…are retained”.
Claim 17 recites “The method of claim 15 wherein the available treatments are…; the available treatments include….; and/or the available treatments include…”, which should be amended to include a colon after the “wherein” in line 1 of the claim to properly indicate the recited list, thus reciting “The method of claim 15: wherein…; wherein…; and/or wherein..”.
Claim 17 recites “the available treatments include modified code status…”in the last line of the claim, which is grammatically incorrect and should be amended to recite “…include a modified code status…”.
Claims 20-21 recite “…wherein genetic sequencing is performed for both biological parents and..”, which should be amended to refer to “for both biological parents of the subject” to increase clarity.
Appropriate correction is required
Claim Interpretation
Claim 1 recites the term “optionally”. Claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed. See MPEP 2111.04 I. Therefore, any limitation following “optionally” is interpreted to be not required by the claim.
Claim 33 recites “…storing on a non-transitory memory the plurality of EMRs, the plurality of phenomes, and the plurality of clinical phenotypes to generate a searchable database”. The phrase “to generate a searchable database” is interpreted to recite an intended use of the stored EMRs, phenomes, and clinical phenotypes, but the claim does not require generating a searchable database. It is noted that claim 34 does then utilize the database, and thus claim 34 is interpreted to require that the database is generated.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1-36 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, regards as the invention.
Claim 1, and claims dependent therefrom, are indefinite for recitation of “available treatments” in both steps g) and h). The term “available” is a relative term which renders the claim indefinite. The term “available” 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. As a result, the metes and bounds of what treatments fall within the metes and bounds of an “available” treatment are not clear. For example, it is not clear if “available treatments” is intended to refer to simply any treatment that could be administered (e.g. pre-clinical treatments), or if the term refers to treatments available to everyone (e.g. clinically approved). Similarly, it is unclear if the term refers to “available” treatments as of the effective filing date of the claimed invention, or if the term refers to any treatment currently “unavailable” but later becomes available. For purpose of examination, the term “available treatment” is interpreted to mean “treatment”.
Claim 8 is indefinite for recitation of “all known genetic diseases”. The metes and bounds of “all known genetic diseases” because it is not clear as to whom or when, the genetic diseases are known. As a result, one of ordinary skill in the art cannot ascertain the metes and bounds of “all known genetic diseases” For purpose of examination the term is interpreted to mean “of genetic diseases expressed in the same vocabulary…”.
Claim 10 is indefinite for recitation of “…wherein the genetic variants are utilized to generate a probabilistic diagnosis”. examples of claim language, although not exhaustive, that may raise a question as to the limiting effect of the language in a claim are "wherein" clauses. The determination of whether each of these clauses is a limitation in a claim depends on the specific facts of the case. See, e.g., Griffin v. Bertina, 285 F.3d 1029, 1034, 62 USPQ2d 1431 (Fed. Cir. 2002) (finding that a "wherein" clause limited a process claim where the clause gave "meaning and purpose to the manipulative steps"). However, the court noted that a "‘whereby clause in a method claim is not given weight when it simply expresses the intended result of a process step positively recited. See MPEP 2111.04 I. In the instant case, it is not clear if the limitation is merely reciting an intended use of the genetic variants, or if the limitation intends to further limit one of the steps of claim 1 relating to determining a differential diagnosis, and thus require actually using the genetic variants to generate the probabilistic diagnosis. Clarification is requested. For purpose of examination, claim the limitation is interpreted to recite an intended use of the genetic variants.
Claims 15-17 recite “the available treatments”. Claim 1, from which claims 15-17 depend, recite “available treatments” at each of steps g) and h), and as a result, it is not clear if “the available treatments” is referring to the available treatments for which efficacy was determined in g) or the available treatments rank ordered with the third list in h), or if these are all intended to refer to the same available treatments. Clarification is requested. For purpose of examination, the available treatments in claims 15-17 are interpreted to refer to either and/or both the treatments in g) and h) of claim 1.
Claim 16 is indefinite for recitation of “…wherein the available treatments are utilized to generate a probabilistic diagnosis”. For the same reasons discussed above for claim 10, it is not clear if the limitation is merely reciting an intended use of the available treatments, or if the limitation intends to further limit one of the steps of claims 1 or 15 and actually require actually utilizing the available treatments to generate the probabilistic diagnosis. Clarification is requested. For purpose of examination, claim the limitation is interpreted to recite an intended use of the available treatments.
Claim 18 is indefinite for recitation of “comparing the second list of potential differential diagnoses corresponding to genomic regions associated with the first list…” in lines 2-3. The grammar of the limitation is unclear, and as a result it is not clear what is being compared. First, if the claim is intends to compare “the second list of potential differential diagnoses corresponding to genomic regions” with the first list, there is insufficient antecedent basis for this limitation in the claim because claims 1 and 15, from which claim 18 depends, does not require the second list of potential differential diagnoses correspond to genomic regions. Alternatively it is not clear if Applicant intends for the limitation to mean comparing the second list to genomic regions associated with the first list. Clarification is requested via claim amendment. Last, given claim 13 (and Applicant’s specification) describe the second list as being generated by comparing annotated variants on a regional genomic basis with corresponding genomic regions associated with the first list, it appears that “the second list of potential differential diagnoses corresponding to genomic regions associated with the first list…” may simply be referring to the generated second list as recited in claim 13 and described in the spec, in which case it is unclear what is being compared with this second list to generate the third list. For purpose of examination, the limitation is interpreted to mean the generated second list corresponding to genomic regions associated with the first list is compared with any information. Clarification is requested.
Claims 20-21 are indefinite for recitation of “The method of claim 1, wherein genetic sequencing is performed for both biological parents, and only results in which trio diplotypes fit…are obtained” and “The method of claim 20, wherein genetic sequencing is performed for both biological parents, wherein parental health status…is used to obtain only results in which parental diplotypes fit…”. Claim 1, from which claims 20-21 depends, recites “performing genetic sequencing of a DNA sample from the subject; e) determining genetic variants of the DNA; f) analyzing the results of (c) and (e);…h) analyzing the results of (f) and (g)…; generating a report comprising results of any of (a)-(h)”. First, it is unclear what results of claim 1, claims 20-21 intend to only include “…trio diplotypes [that] fit a known inheritance pattern” or “…parental diplotypes [that] fit a known inheritance pattern” (e.g. the determined variants, the results of f), the results of h)?). Furthermore, because claims 20-21 do not refer to “the genetic sequencing”, it is further unclear if claims 20-21 require that the method further comprises performing sequencing for both biological parents (e.g. “wherein the genetic sequencing comprises performing sequencing for both biological parents), or if the wherein clause is simply describing the process in which the “results” were previously obtained such that the genetic variant results, results of (f), results of (h), or results of any (a)-(h) are required to be determined using sequencing data of both parents. Clarification of requested. For purpose of examination, claims 20-21 are interpreted to mean any of the results of claim 1 are obtained using trio/parental diplotypes fitting a known inheritance pattern determined using genetic sequencing, but the claims do not require an active step of sequencing for both parents.
Claim 21, and claims dependent therefrom, are indefinite for recitation of “…wherein parental health status (healthy or affected) is used…”. The phrase "(healthy or affected)” renders the claim indefinite because it is unclear whether the phrase is part of the claimed invention, or if the claims encompass any health status. See MPEP § 2173.05(d). For purpose of examination, the phrase is interpreted to not be required by the claim, and instead is considered exemplary or optional.
Claim 22 is indefinite for recitation of “the parental genome”. Claim 20, from which claim 21 depends requires sequencing both biological parents and as a result, it is not clear which parental genome “the parental genome” is referring to.
Claims 25 and 27 are indefinite for recitation of “the potential differential diagnoses”. Claim 1, from which claims 25 and 27 depend, recites “a first list of potential differential diagnoses”, “a second list of potential differential diagnoses” and “a third list of potential differential diagnoses” and therefore, it is not clear which potential differential diagnoses claims 25 and 27 are referring to, or if claims 25 and 27 intend to refer to the potential differential diagnoses for each of the first, second, and third lists. Clarification is requested. For purpose of examination, claims 25 and 27 are interpreted to refer to any one or more of the potential differential diagnoses.
Claim 33, and claims dependent therefrom, are indefinite for recitation of “the plurality of clinical phenotypes”. Claim 1 already requires the phenome of the subject comprises “a plurality of clinical phenotypes” and claim 32, from which claim 33 depends recites “(a) is performed for a plurality of subjects thereby generating….a plurality of phenomes, and a plurality of clinical phenotypes”. As a result, it is unclear if “the plurality of clinical phenotypes” in claim 33 is referring to the plurality of clinical phenotypes of the subject of claim 1 or for the plurality of subjects of claim 32.
Claim 35 is indefinite for recitation of “…wherein one or more of (a)-(k) are adjustable by a user to determine available diagnoses and available treatments based on the available diagnoses to provide dynamic treatment to the subject”. The metes and bounds of the method steps of (a)-(k) being “adjustable by a user” to determine diagnoses and treatments is not clear. It is not clear in what way each of the steps are intended to be “adjustable”. Claim 1 already uses the transitional phrase “comprising”, which means the claim is open to unrecited elements; it is unclear if claim 35 simply means claim 1 can include additional steps, which is already true, or if the claim intends to require one or more of (a)-(h) involves determining an available diagnosis/treatments. Alternatively, it is unclear if claim 35 is simply reciting an intended use of the method of claim 1 (i.e. the method can be changed to determine available diagnoses/treatments). For purpose of examination, the limitation is interpreted to recite any intended use or result of the method of claim 1 (e.g. the steps can be adjusted).
Claim 36 is indefinite for recitation of “…a controller including a processor and non-transitory memory, wherein the controller is configured to perform any one, or combination of (a)-(k) of claim 1”. Claim 1 recites “d) performing genetic sequencing of a DNA sample from the subject”, which is beyond the scope of what a controller comprising a processor and memory can perform. As a result, it’s unclear if “the controller configured to” perform sequencing is intended to require that the controller includes additional hardware for sequencing a sample, or if the controller is intended to only receive sequencing data of a DNA sample from the subject. For purpose of examination, the limitation will be interpreted to mean the controller is configured to receive sequencing data.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 6, 10, 16, and 35-36 are rejected under 35 U.S.C. 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 6 recites “wherein the DNA sample is from a biological sample”. Claim 1, from which claim 6 ultimately depends, recites sequencing “a DNA sample from the subject”. Given the DNA sample is from the subject, the DNA sample is inherently from a biological sample (i.e. from the subject), and thus claim 6 fails to further limit the subject matter of claim 5, from which it depends.
Claim 10 recites “…wherein the genetic variants are utilized to generate a probabilistic diagnosis and/or are annotated and classified…”, and thus only requires the limitation of “wherein the genetic variants are utilized to generate a probabilistic diagnosis” under the broadest reasonable interpretation of the claim. As discussed above, under 35 U.S.C. 112(b), the limitation is interpreted as an intended use of the genetic variants. However, claim 10 does not actually require utilizing the variants to generate a probabilistic diagnosis. As a result, claim 10 fails to further limit the subject matter of claim 9, from which it depends, under the broadest reasonable interpretation of the claim.
Claim 16 recites “wherein the available treatments are utilized to generate a probabilistic diagnosis”, which merely recites an intended result of the available treatments and thus are not given patentable weight, as discussed above under 35 U.S.C. 112(b). Therefore, claim 16 fails to further limit the subject matter of claim 16, from which it depends.
Claim 35 recites “The method of claim 1, wherein one or more of (a)-(k) are adjustable by a user to determine…”, which has been interpreted as an intended use of the claimed method as discussed above under 35 U.S.C. 112(b). Claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed, or by claim language that does not limit a claim to a particular structure. See MPEP 2111.04 I. Therefore, claim 3 fails to further limit the subject matter of claim 1, from which it depends.
Claim 36 recites “A system comprising: a controller including…the controller is configured to perform any one, or combination of (a)-(k) of claim 1”. Claim 36 depends, from claim 1, but does not require all the limitations of claim 1. Therefore, claim 36 is not a proper dependent claim because it does not include the limitations of base claim 1. See MPEP 608.01(n) III regarding instances where a dependent claim is a different statutory class as the independent claim, explaining “if claim 1 recites a method of making a specified product, a claim to the product set forth in claim 1 would not be a proper dependent claim if the product can be made by a method other than that recited in the base method claim, and thus, does not include the limitations of the base claim”.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-36 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claims 1 and 36 being representative) is directed to a method and system. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Claim 1 recites the following steps which fall under the mental processes groupings of abstract ideas:
(a) determining a phenome of a subject from an electronic medical record (EMR), wherein the phenome comprises a plurality of clinical phenotypes extracted from the EMR;
(b) translating the clinical phenotypes into a standardized vocabulary;
c) generating a first list of potential differential diagnoses of the subject, the first list optionally being rank ordered;
e) determining genetic variants of the DNA; f) analyzing the results of (c) and (e) to generate a second list of potential differential diagnoses of the subject, the second list being rank ordered;
g) determining the efficacy and/or quality of evidence of efficacy of available treatments for the second list of potential differential diagnoses;
h) analyzing the results of (f) and (g) to generate a third list of potential differential diagnoses of the subject, the third list being rank ordered, together with available treatments; and
i) generating a report comprising results of any of (a)-(h).
Independent claim 36 recites the same abstract ideas in (a)-(c) and (e)-(i) of claim 1 above.
The identified claim limitations falls into the groups of abstract ideas of mental processes for the following reasons. In this case, step (a) can be practically performed in the mind by reading an EMR of the subject and determining clinical phenotypes associated with the subject. Step (b) translating encompasses simply analyzing the clinical phenotypes and converting the names for each phenotype to a consistent nomenclature, which amounts to a mere analysis of data. Generating a list of potential differential diagnoses (c) can be practically performed in the mind by organizing and writing the clinical phenotypes of the subject into a list. The step of determining genetic variants of the DNA is broadly recited and encompasses comparing sequences of the subject to a reference to identify differences, similar to the claims to "comparing BRCA sequences and determining the existence of alterations," where the claims cover any way of comparing BRCA sequences such that the comparison steps can practically be performed in the human mind, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 763, 113 USPQ2d 1241, 1246 (Fed. Cir. 2014). Analyzing the first list and the generated variants to generate a second ranked list of differential diagnoses can be practically performed in the mind by identifying differential diagnoses of the first list that are associated with pathogenic variants, and ranking the diagnoses based on the subject having a pathogenic variant. Determining efficacy of available treatments for the second ranked list encompasses analyzing treatments for each diagnosis in the list and reading published information to determine how well each treatment works, which is a mental process. Similar to step f), analyzing the results of the second ranked list and the determined efficacy to determine a third ranked list of differential diagnoses with available treatments encompasses identifying diagnoses with an available treatment and ordering the treatments based on the efficacy of the treatment in the list. Last, generating a report comprising results of any of (a)-(h) can be practically performed in the mind aided by pen and paper by simply organizing the information of any of steps (a)-(h). Overall, claim 1 recites an abstract idea analogous to "collecting information, analyzing it, and displaying certain results of the collection and analysis," where the data analysis steps are recited at a high level of generality such that they could practically be performed in the human mind, Electric Power Group v. Alstom, S.A., 830 F.3d 1350, 1353-54, 119 USPQ2d 1739, 1741-42 (Fed. Cir. 2016).
Dependent claims 2, 4, 8-9, 11-15, 17-25, 27-28, 30-32, and 34 further recite an abstract idea and/or further limit the abstract idea of claim 1 above. Dependent claim 2 further recites the mental process and certain method of organizing human activity of generating the EMR for the subject prior to (a), which involves organizing information into a record, similar to the actions a physician would carry out on a patient. Dependent claim 4 further limits the mental process of (a)-(c) and (d) and (e) to be performed simultaneously (e.g. mentally by two different people). Dependent claim 8 further limits the mental process of generating the first, second and/or third ranked list to be by querying (e.g. reading) a database. Dependent claim 9 further recites the mental process of annotating and classifying pathogenicity of variants. Dependent claim 11 further limits the mental process of analyzing variants to only retain certain variants. Dependent claim 12 further recites the mental process of annotating variants to identify and rank diplotypes based on pathogenicity. Dependent claim 13 further limits the mental process of determining the second list to comprise performing data comparisons. Dependent claim 14 further limits the mental process of determining variants to determine ranked variants. Dependent claims 15 and 17 further recites the mental process of annotating and classifying treatments into particular categories. Dependent claim 18 further limits the mental process of generating the third list to comprise performing data comparisons. Dependent claim 19 further recites the mental process of j) determining the availability of confirmatory tests for the third list, and under the broadest reasonable interpretation of the claim, none of the other limitations of the claim are required. Dependent claims 20-21 further limits the mental process of determining variants to only obtain certain results fitting a known inheritance pattern determined by parental sequencing. Dependent claim 22 further limits the mental process of determining a diagnosis of claim 1 to only use variants in the subject’s genome, but not the parental genome. Dependent claims 23-24 further limits the mental process of claim 1 to be performed on information for a particular subject. Dependent claims 25 and 28 further limit the mental process of determining a diagnosis to determine a genetic diagnosis or cancer diagnosis. Dependent claims 27 further recites the mental process of generating a therapy regime for the subject. Dependent claim 30 further recites the mental process of analyzing supplemental clinical information to determine the phenome. Dependent claims 30-31 further limit the mental process of (a) to be performed for multiple subjects. Dependent claim 34 further recites the mental process of using a database to screen for information. Therefore, claims 1-36 recite an abstract idea. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, the Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s), and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception. This judicial exception is not integrated into a practical application for the following reasons.
Dependent claims 2, 4, 8-9, 11-15, 17-25, 28, 30-32, and 34 recite an abstract idea, but do not recite elements in addition to the judicial exception. Dependent claims 10, 16, and 35 fail to further limit the subject matter of claim 1, from which they depend, and are part of the abstract idea of claim 1.
The additional elements of claims 1 and 5-7 include:
d) performing genetic sequencing of a DNA sample from the subject;
wherein [the] genetic sequencing comprises, genome sequencing, rapid whole genome sequencing (rWGS), ultra-rapid whole genome sequencing, exome sequencing, or rapid whole exome sequencing (rWES) (claim 5); and
the DNA sample is from a biological sample, wherein the [biological] sample is blood, dried blood spot, serum, saliva, buccal smear/swab, plasma, feces, cerebrospinal fluid or urine (claims 6-7).
The additional elements of performing genome sequencing on a blood, serum, or saliva, etc. sample of a subject only serves to collect data for use by the abstract idea, which does not integrate the recited judicial exception into a practical application. See MPEP 2106.05(g).
The additional element of claims 26, 33, and 36 include:
wherein the method is automated (claim 26);
storing on a non-transitory memory the plurality of EMRs, the plurality of phenomes, and the plurality of clinical phenotypes to generate a searchable database (claim 33).
a controller including at least one processor and non-transitory memory (claim 36).
The additional element of claim 3 includes:
wherein (b) utilizes natural language processing to perform the translation.
The additional elements of a processor for automating the method, a non-transitory memory, and storing information are generic computer components and/or processes. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application. See MPEP 2106.05(f). Further regarding “utilizing natural language processing” to perform (b), this limitation amounts to mere instructions to apply the translating step (b) on a computer (see MPEP 2106.05(f), and furthermore, merely indicates a technological field (i.e. NLP) in which to apply the abstract idea, which cannot integrate the judicial exception into a practical application.
The additional element of claims 27 and 29 include:
providing a therapy to the subject;
wherein the therapy is selected from the group consisting of surgery, adjuvant chemotherapy, neoadjuvant chemotherapy, radiation therapy, hormone therapy, cytotoxic therapy, immunotherapy, adoptive T cell therapy, targeted therapy, or any combinations thereof.
The additional element of providing a therapy to the subject does not integrate the recited judicial exception into a practical application for the following reasons. First, Claim 27 does not require providing the therapy, and instead encompasses only “generating a therapy regime”, which is part of the abstract idea. Therefore, this limitation is not required by the claim. Furthermore, even if the providing step was required, MPEP 2106.04(d)(2) states in order to qualify as a "treatment" or "prophylaxis" limitation for purposes of this consideration, the claim limitation in question must affirmatively recite an action that effects a particular treatment or prophylaxis for a disease or medical condition. For example, a step of "prescribing a topical steroid to a patient with eczema" is not a positive limitation because it does not require that the steroid actually be used by or on the patient. In the instant case, simply providing a therapy does not require the therapy is actually used by the patient, and thus the limitation does not integrate the recited judicial exception into the practical application of effecting a particular treatment.
Therefore, the additionally recited elements amount to insignificant extra-solution activity and, as such, the claims as a whole do no integrate the abstract idea into practical application. Thus, claims 1-36 are directed to an abstract idea. [Step 2A, Prong 2: NO]
Step 2B: In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. See MPEP § 2106.05.
The claims do not include any additional steps appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception.
Therefore, the additional element is not sufficient to amount to significantly more than the judicial exception.
Dependent claims 2, 4, 8-9, 11-15, 17-25, 28, 30-32, and 34 recite an abstract idea, but do not recite elements in addition to the judicial exception. Dependent claims 10, 16, and 35 fail to further limit the subject matter of claim 1, from which they depend, and are part of the abstract idea of claim 1.
The additional elements of claims 1 and 5-7 include:
d) performing genetic sequencing of a DNA sample from the subject;
wherein [the] genetic sequencing comprises, genome sequencing, rapid whole genome sequencing (rWGS), ultra-rapid whole genome sequencing, exome sequencing, or rapid whole exome sequencing (rWES) (claim 5); and
the DNA sample is from a biological sample, wherein the [biological] sample is blood, dried blood spot, serum, saliva, buccal smear/swab, plasma, feces, cerebrospinal fluid or urine (claims 6-7).
Performing genome sequencing on a biological sample, such as a blood sample, of a subject is well-understood, routine, and conventional. This position is supported by Applicant’s own specification at para. [0080]-[0081], which explains that sequencing may be performed by any method known in the art, including shotgun sequencing (i.e. genome sequencing), massively parallel sequencing, whole genome sequencing, etc., and discloses a plurality of commercially available platforms for performing the sequencing. Applicant’s specification at para. [0129] also explains that conventional clinical genome sequencing requires preparatory steps of purifying DNA from blood of a patient, demonstrating the conventionality of sequencing DNA in a blood sample. Applicant’s specification at para. [0131] discloses commercially available software for analyzing sequencing data, further demonstrating the conventionality of sequencing with computer components.
The additional element of claims 26, 33, and 36 include:
wherein the method is automated (claim 26);
storing on a non-transitory memory the plurality of EMRs, the plurality of phenomes, and the plurality of clinical phenotypes to generate a searchable database (claim 33).
a controller including at least one processor and non-transitory memory (claim 36).
The additional elements of a processor for automating the method, a non-transitory memory, and storing information are generic computer components and/or processes. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit). Further regarding performing (b) using NLP, as explained by the Supreme Court, a claim directed to a judicial exception cannot be made eligible "simply by having the applicant acquiesce to limiting the reach of the patent for the formula to a particular technological use." Diamond v. Diehr, 450 U.S. 175, 192 n.14, 209 USPQ 1, 10 n. 14 (1981). Thus, limitations that amount to merely indicating a field of use or technological environment in which to apply a judicial exception do not amount to significantly more than the exception itself. See MPEP 2106.05(h).
The additional element of claims 27 and 29 include:
providing a therapy to the subject;
wherein the therapy is selected from the group consisting of surgery, adjuvant chemotherapy, neoadjuvant chemotherapy, radiation therapy, hormone therapy, cytotoxic therapy, immunotherapy, adoptive T cell therapy, targeted therapy, or any combinations thereof.
The additional element of providing a therapy to the subject does not provide significantly more for the following reasons. First, Claim 27 does not require providing the therapy, and instead encompasses only “generating a therapy regime”, which is part of the abstract idea. Therefore, this limitation is not required by the claim, and as a result, cannot provide significantly more.
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself. [Step 2B: NO]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea (and/or natural correlation) without significantly more. For additional guidance, applicant is directed generally to applicant is directed generally to the MPEP § 2106.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim 36 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kingsmore (2018).
Cited reference: Kingsmore et al. US 2019/0325988 A1 (cited on IDS filed 17 Jan. 2023); Pub. Date: 18 April 2019.
Regarding claim 36, Kingsmore discloses a controller including at least one processor and non-transitory memory, wherein the controller is configured to perform (a)-(c) and (e)-(g) (claim 37) as follows:
Kingsmore discloses a) determining a phenome of a subject from an electronic medical record (EMR), wherein the phenome comprises a plurality of clinical phenotypes extracted from the EMR (claim 1; [0007]) (i.e. the controller performs any one of (a)-(k), here (a)).
Kingsmore discloses b) translating the clinical phenotypes into standardized vocabulary; (claim 1; [0008]).
Kingsmore discloses c) generating a first list of potential differential diagnoses of the subject ([0009]; claim 1).
Kingsmore discloses e) determining genetic variants of the DNA (claim 1; [0011]).
Kingsmore discloses f) analyzing the results of (c) and (e) to generate a second list of potential differential diagnoses of the subject, the second list being rank ordered (claim 1; [0012]).
Kingsmore discloses g) generating a report comprising results of the analysis of (f).
Therefore, Kingsmore anticipates the claimed invention.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-35 are rejected under 35 U.S.C. 103 as being unpatentable over Kingsmore (2019) in view of Schmidt (2012).
Cited references:
Kingsmore et al. US 2019/0325988 A1 (cited on IDS filed 17 Jan. 2023); and
Schmidt et al. US 2012/0232930 A1.
Regarding claim 1, Kingsmore discloses a method comprising the following steps (Abstract; claim 1)
Kingsmore discloses a) determining a phenome of a subject from an electronic medical record (EMR), wherein the phenome comprises a plurality of clinical phenotypes extracted from the EMR (claim 1; [0007]).
Kingsmore discloses b) translating the clinical phenotypes into standardized vocabulary; (claim 1; [0008]).
Kingsmore discloses c) generating a first list of potential differential diagnoses of the subject ([0009]; claim 1).
Kingsmore discloses d) performing genetic sequencing of a DNA sample from the subject (claim1; [0010]).
Kingsmore discloses e) determining genetic variants of the DNA (claim 1; [0011]).
Kingsmore discloses f) analyzing the results of (c) and (e) to generate a second list of potential differential diagnoses of the subject, the second list being rank ordered (claim 1; [0012]).
Kingsmore discloses (g) determining or identifying a disease status comprising easing the efficacy of one or more treatment programs of a disease ([0076])
Kingsmore discloses i) generating a report comprising results of the analysis of (f) (claim 1; [0013]).
Further regarding claims 1 and dependent claims 15-17, 19, and 28, Kingsmore does not disclose the following:
Regarding claim 1, Kingsmore does not disclose h) analyzing the results of (f) and (g) to generate a third list of potential differential diagnoses of the subject, the third list being rank ordered, together with available treatments.
Regarding claims 15-17, Kingsmore does not disclose (h) further comprises annotating and classifying the available treatments, wherein the available treatments are annotated and classified as being safe and effective (SE). It is noted claim 16 fails to further limit the subject matter of claim 15, from which it depends for the reasons discussed under 35 U.S.C. 112(d), and therefore, claim 16 is addressed with claim 15 below.
Regarding claim 19, Kingsmore does not disclose j) determining the availability of confirmatory tests for the third list of potential differential diagnoses.
Regarding claim 28, Kingsmore does not disclose the potential differential diagnoses comprise cancer.
However, Kingsmore does disclose determining or identifying a disease status comprising easing the efficacy of one or more treatment programs of a disease ([0076]) and further discloses the evidence supporting a diagnoses was manually evaluated by an expert, and if rWGS or rWES established a provisional diagnoses (i.e. a diagnosis of the second list) for which a specific treatment was available, this was immediately conveyed to the clinical team ([0085]). This demonstrates extracting a diagnosis with an available treatment from the second list.
Furthermore, regarding claim 1, Schmidt discloses a clinical decision support system for analyzing electronic health records of patient to provide differential diagnoses for a patient in addition to available therapies (Abstract; FIG. 3). Schmidt discloses generating and displaying a ranked list of differential diagnoses together with available therapy options ranked by effectiveness (i.e. analyzing (f) and (g) to generate a third rank ordered list together with available treatments) ([0042]; FIG. 3, e.g. diagnoses #32, ranked by probability #25 together with therapy options #34).
Regarding claims 15-17, Schmidt further discloses generating the list of differential diagnoses with available therapy options comprises annotating each available treatment with additional diagnostics and classifying each treatment with a probability of success (FIG. 3, #29 probabilities and “Rd”, “Pr”, etc. annotations under each treatment; [0045]). Schmidt discloses the treatments are annotated based on a quality of life of the patient (i.e. safe for the patient/ lower adverse events) and survival time (i.e. effectiveness), with higher probabilities of success of a therapy indicating higher quality measures of higher quality of life and higher effectiveness ([0059]).
Regarding claim 19, Schmidt further discloses further determining recommended diagnostics with each therapy option in order to refine the current diagnosis (i.e. determining availability of confirmatory tests) ([0045]; [0054] Fig. 3)).
Regarding claim 28, Schmidt further discloses the differential diagnoses include cancer (Fig. 3; [0042]; [0052]; [0054]).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Kingsmore, to have further generated a third ranked differential diagnoses list, including cancer, together with the annotated and classified available treatments and determining available confirmatory tests for the list, as shown by Schmidt above, thus arriving at the inventions of claims 1, 15-17, 19, and 28. One of ordinary skill in the art would have been motivated to combine the methods of Kingsmore and Schmidt in order to assist a physician in determining the optimal sequence of clinical actions from diagnosis to therapy for cancer, as shown by Schmidt ([0030]). This modification would have had a reasonable expectation of success given both Kingsmore and Schmidt analyze data to determine a list of differential diagnoses of a subject, Kingsmore discloses analyzing available treatments of the diagnoses of the second list, and thus the information and display of Schmidt is applicable to the method of Kingsmore.
Regarding the dependent claims:
Regarding claim 2, Kingsmore discloses generating the EMR for the subject prior to (a) (claim 2).
Regarding claim 3, Kingsmore discloses (b) utilizes natural language processing to perform the translation (claim 3).
Regarding claim 4, Kingsmore discloses (a)-(c) and (d)-(e) are performed in parallel (claim 4).
Regarding claim 5, Kingsmore discloses genetic sequencing comprises rapid whole genome sequencing (rWGS), ultra-rapid whole genome sequencing, or rapid whole exome sequencing (rWES) (claim 5);
Regarding claim 6, Kingsmore discloses the DNA sample is from a biological sample (claim 6).
Regarding claim 7, Kingsmore discloses the sample is serum, saliva, buccal smear/swab, plasma, feces, cerebrospinal fluid or urine (claim 7).
Regarding claim 8, Kingsmore discloses the second ranked list is performed (generated) via query of a database populated with known clinical phenotypes expressed in the same vocabulary as the standardized vocabulary of (b) (claim 11).
Regarding claim 9, Kingsmore discloses determining genetic variants of (f) further comprises annotation and classification of the genetic variants (claim 12).
Regarding claim 10, Kingsmore discloses the genetic variants are utilized to generate a probabilistic diagnosis (claim 13) and further discloses the genetic variants are annotated and classified as being of uncertain significance (VUS), pathogenic (P) or likely pathogenic (LP) (claim 14).
Regarding claim 11, Kingsmore discloses only genetic variants with an allele frequency of <5%, 2.5%, 1%, 0.1% or less in a population of healthy individuals is retained (claim 15).
Regarding claim 12, Kingsmore discloses the determining genetic variants of (e) further comprises annotation of the genetic variants to identify and rank all diplotypes as being of uncertain significance (VUS), pathogenic (P) or likely pathogenic (LP) on the basis of pathogenicity (claim 16).
Regarding claim 13, Kingsmore discloses the second list of potential differential diagnoses is generated by comparing the annotated VUS, LP and P diplotypes on a regional genomic basis with corresponding genomic regions associated with the first list of potential differential diagnoses of (c) (claim 17).
Regarding claim 14, Kingsmore discloses the genetic variants are ranked based on a combination of rank of goodness of fit of clinical phenotypes, rank of pathogenicity of diplotypes, and/or allele frequencies of the genetic variants in a population of health individuals (claim 18).
Regarding claim 18, Kingsmore further discloses determining the second list of potential differential diagnoses by comparing annotated diplotypes on a regional basis with corresponding genomic regions associated with the first list of potential differential diagnoses (claim 17; [0050]), such that the second list of potential differential diagnoses is corresponding to genomic regions associated with the first list of potential differential diagnoses. Furthermore, Kingsmore in view of Schmidt make obvious comparing this differential diagnosis list with probability information and available treatment information to generate a third ranked differential diagnoses list with available treatments, as applied above.
Regarding claim 20, Kingsmore discloses the genetic sequencing is performed for both biological parents and only results in which trio diplotypes fit a known inheritance pattern of a specific genetic disease are obtained (claim 20).
Regarding claim 21¸Kingsmore discloses the genetic sequencing is performed for both biological parents, wherein parental health status (healthy or affected) is used to obtain only results in which parental diplotypes fit a known inheritance pattern of a specific genetic disease (claim 21).
Regarding claim 22, Kingsmore discloses the genetic variants present in the subject's genome and not in the parental genome are utilized to determine a diagnosis for the subject (claim 22).
Regarding claim 23, Kingsmore discloses the subject is less than 5 years old (claim 24).
Regarding claim 24, Kingsmore discloses the subject is an infant, fetus or neonate (claim 25).
Regarding claim 25, Kingsmore discloses the potential differential diagnoses comprise genetic diseases (claim 26).
Regarding claim 26, Kingsmore discloses the method is automated (claim 27).
Regarding claim 27, Kingsmore discloses generating a therapy regime for the subject based on (g) (claim 28) or providing a therapy to the subject (claim 29).
Regarding claim 29, claim 27, from which claim 29 depends, recites alternative embodiments of generating a therapy regime for the subject or providing a therapy to the subject. Because Kingsmore discloses the embodiment of generating a therapy regime for the subject, the step of providing a therapy to the subject is not required, including the specific therapies provided by claim 29. Therefore claim 29 is rejected for the same reasons as claim 27-28. Regardless, it is noted that Kingsmore in view of Schmidt make obvious providing a surgery or radiation therapy to the subject ([0042]; FIG. 3 of Schmidt), as applied to claims 1 and 28 above.
Regarding claim 30, Kingsmore discloses analyzing supplemental clinical information to determine the phenome (claim 30).
Regarding claim 31, Kingsmore discloses (a) is performed for a plurality of subjects thereby generating a plurality of EMRs, a plurality of phenomes, and a plurality of clinical phenotypes (claim 31).
Regarding claim 32, Kingsmore discloses (a) is performed for a plurality of subjects thereby generating a plurality of EMRs, a plurality of phenomes, and a plurality of clinical phenotypes (claim 32).
Regarding claim 33, Kingsmore discloses storing on a non-transitory memory the plurality of EMRs, the plurality of phenomes, and the plurality of clinical phenotypes to generate a searchable database (claims 33-34).
Regarding claim 34, Kingsmore discloses utilizing the database to screen for genetic data, a genotype, or a disease or disorder in a second subject or to update a diagnosis of the subject (claims 35-36).
Regarding claim 35, claim 35 fails to further limit the subject matter of claim 1 as discussed in the 112(d) rejection above. Therefore, claim 35 is rejected for the same reasons discussed above for claim 1.
Therefore, the invention is prima facie obvious.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 36 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4, 7-9, 11, 13-22, 24-25, 27-44 of copending Application No. 16/388,614 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because:
Regarding instant claim 36, reference claims 1 and 37 disclose the limitations of instant claim 36. It is noted that reference claims 1 and 37 require additional limitations, and have a different scope.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1-35 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4, 7-9, 11, 13-22, 24-25, 27-44 of copending Application No. 16/388,614 in view of Schmidt (2012).
Cited reference: Schmidt et al. US 2012/0232930 A1.
Regarding instant claim 1, reference claim 1 discloses the limitations of instant claim 1, and administering a targeted treatment based on the diagnosis in (k), which generally discloses assessing available treatments.
Further regarding instant claims 1 and dependent instant claims 15-17, 19, and 28, the reference claims do not disclose the following:
Regarding instant claim 1, the reference claims do not disclose h) analyzing the results of (f) and (g) to generate a third list of potential differential diagnoses of the subject, the third list being rank ordered, together with available treatments.
Regarding instant claims 15-17, the reference claims do disclose (f) analyzing the results of (c) and (e) to generate a third (h) further comprises annotating and classifying the available treatments, wherein the available treatments are annotated and classified as being safe and effective (SE). It is noted claim 16 fails to further limit the subject matter of claim 15, from which it depends for the reasons discussed under 35 U.S.C. 112(d), and therefore, claim 16 is addressed with claim 15 below.
Regarding instant claim 19, the reference claims do not disclose j) determining the availability of confirmatory tests for the third list of potential differential diagnoses.
Regarding instant claim 28, the reference claims do not disclose the potential differential diagnoses comprise cancer.
Furthermore, regarding instant claim 1, Schmidt discloses a clinical decision support system for analyzing electronic health records of patient to provide differential diagnoses for a patient in addition to available therapies (Abstract; FIG. 3). Schmidt discloses generating and displaying a ranked list of differential diagnoses together with available therapy options ranked by effectiveness (i.e. analyzing (f) and (g) to generate a third rank ordered list together with available treatments) ([0042]; FIG. 3, e.g. diagnoses #32, ranked by probability #25 together with therapy options #34).
Regarding instant claims 15-17, Schmidt further discloses generating the list of differential diagnoses with available therapy options comprises annotating each available treatment with additional diagnostics and classifying each treatment with a probability of success (FIG. 3, #29 probabilities and “Rd”, “Pr”, etc. annotations under each treatment; [0045]). Schmidt discloses the treatments are annotated based on a quality of life of the patient (i.e. safe for the patient/ lower adverse events) and survival time (i.e. effectiveness), with higher probabilities of success of a therapy indicating higher quality measures of higher quality of life and higher effectiveness ([0059]).
Regarding instant claim 19, Schmidt further discloses further determining recommended diagnostics with each therapy option in order to refine the current diagnosis (i.e. determining availability of confirmatory tests) ([0045]; [0054] Fig. 3)).
Regarding instant claim 28, Schmidt further discloses the differential diagnoses include cancer (Fig. 3; [0042]; [0052]; [0054]).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of the reference claims, to have further generated a third ranked differential diagnoses list, including cancer, together with the annotated and classified available treatments and determining available confirmatory tests for the list, as shown by Schmidt above, thus arriving at the inventions of instant claims 1, 15-17, 19, and 28. One of ordinary skill in the art would have been motivated to combine the methods of the reference claims and Schmidt in order to assist a physician in determining the optimal sequence of clinical actions from diagnosis to therapy for cancer, as shown by Schmidt ([0030]). This modification would have had a reasonable expectation of success given both the reference claims and Schmidt analyze data to determine a list of differential diagnoses of a subject, and thus the information and display of Schmidt is applicable to the method of the reference claims.
Reference claims 2-4 disclose the limitations of instant claims 2-4.
Reference claim 1 discloses the limitation of instant claims 5-6.
Reference claim 7 discloses the limitation of instant claim 7.
Reference claim 11 discloses the limitation of instant claim 8.
Reference claim 14-18 discloses the limitation of instant claims 9-15.
Regarding instant claim 18, reference claim 17 discloses determining the second list of potential differential diagnoses by comparing annotated diplotypes on a regional basis with corresponding genomic regions associated with the first list of potential differential diagnoses, such that the second list of potential differential diagnoses is corresponding to genomic regions associated with the first list of potential differential diagnoses. Furthermore, the reference claims in view of Schmidt make obvious comparing this differential diagnosis list with probability information and available treatment information to generate a third ranked differential diagnoses list with available treatments, as applied above.
Reference claims 20-22 disclose the limitation of instant claims 20-22.
Reference claims 24-25 disclose the limitation of instant claims 23-24
Reference claim 1 discloses the limitation of instant claim 25.
Reference claim 27-28 the limitation of instant claims 26-27 and 29.
Reference claims 30-34 discloses the limitation of instant claims 30-34.
Regarding instant claim 35, the claim fails to further limit the subject matter of instant claim 1, and thus is rejected for the same reasons as instant claim 1.
This is a provisional nonstatutory double patenting rejection.
Conclusion
No claims are allowed.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685