DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of Group IV (claims 55-58) in the reply filed on 11/04/2025 is acknowledged.
Claims 1-15, 31, 43-48, and 54 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 11/04/2025.
New claims 70-80 were added in the reply filed on 11/04/2025. Applicant asserts that new claims 70-80 depend on elected claim 55, thereby reading on and encompassing the elected invention. Upon review of the claim set filed 11/04/205, the Examiner concurs that new claims 70-80 encompass the elected invention. Accordingly, claims 55-58 and 70-80 are pending and under consideration.
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. The earliest effective filing date to which the instant application is entitled is 10/16/2019.
Information Disclosure Statement
Receipt of information disclosure statements on 11/04/2022 and 11/04/2025 is acknowledged.
The information disclosure statement filed 11/04/2022 fails to comply with 37 CFR 1.98(a)(2), which requires a legible copy of each cited foreign patent document; each non-patent literature publication or that portion which caused it to be listed; and all other information or that portion which caused it to be listed. While the IDS filed 11/04/2022 lists Sirr et al., 2020 (reference 23), the uploaded document is Sirr et al., 2018. Accordingly, the information disclosure statements have been placed in the application file, but the information referred to therein has not been considered.
Drawings
The drawings are objected to because:
Regarding Figure 4, the text in the table is of insufficient quality to be clearly legible. It would be remedial to increase the image quality in the table such that the text is clearly legible. Furthermore, while the brief description at paragraph [0045] of the instant specification indicates that Figure 4 depicts a bar graph that shows the measurement of the growth of yeast cells expressing six different PSAT mutations, this description does not clarify the identity of the y axis, nor does it identify all seven bars in the bar graph. It would be remedial to label the axes of Figure 4 such that one of ordinary skill in the art can readily interpret the Figure in view of the associated brief description.
Regarding Figure 6, while the brief description at paragraph [0047] of the instant specification indicates that Figure 6 shows a qualitative assay of testing disease alleles individually, this description does not aid someone of ordinary skill in the art in interpreting the bar graph presented in Figure 6, which is devoid of any labeling. It would be remedial to label Figure 6 such that one of ordinary skill in the art can readily interpret the Figure in view of the associated brief description.
Regarding Figure 7, while the brief description at paragraph [0048] of the instant specification indicates that Figure 7 depicts a growth assay, this description does not clarify the identity of the y axis. It would be remedial to label the axes of Figure 7 such that one of ordinary skill in the art can readily interpret the Figure in view of the associated brief description.
Regarding Figure 8, the text labeling the threshold values is of insufficient quality to be clearly legible. It would be remedial to increase the image quality such that the text is clearly legible. Furthermore, while the brief description at paragraph [0049] of the instant specification indicates that Figure 8 depicts a bar graph that shows the measurement of the growth of yeast cells expressing six different PSAT mutations, this description does not clarify the identity of the y axis. It would be remedial to label the axes of Figure 8 such that one of ordinary skill in the art can readily interpret the Figure in view of the associated brief description.
Regarding Figure 9, while the brief description at paragraph [0050] of the instant specification indicates that Figure 9 depicts a bar graph that shows the measurement of the growth of haploid strains containing various PSAT1 variants, this description does not clarify the identity of the y axis. It would be remedial to label the axes of Figure 9 such that one of ordinary skill in the art can readily interpret the Figure in view of the associated brief description.
Regarding Figures 10-18, while the associated brief descriptions at paragraphs [0051]-[0059] indicate that these Figures depict “personalized yeast models,” this description does not clarify the identity of the y axis. It would be remedial to label the axes of Figures 10-18 such that one of ordinary skill in the art can readily interpret the Figure in view of the associated brief description.
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
The disclosure is objected to because of the following informalities:
The tables of the instant specification are listed as Table 1 (paragraph [0112]), Table 2 (paragraph [0121]), and then Table 0.2 (paragraph [0135]), Table 0.3 (paragraph [0138]), Table 0.4 (paragraph [0219]), and Table 0.5 (paragraph [0220]). This numbering is unconventional and improper. It would be remedial to re-number the Tables consecutively such that they are numbered as Table 1, Table 2, Table 3, etc.
The paragraph numbering at paragraph [0232] erroneously includes labeling for both paragraph [0232] and [0274]. Given that the paragraph at issue is flanked by paragraphs [0231] and [0233], it would be remedial to re-number paragraph [0232] such that it is identified only as paragraph [0232].
Appropriate correction is required.
Claim Objections
Claims 55, 56, 58, and 77-79 are objected to because of the following informalities:
Claim 55 does not comport with standard grammatical and/or linguistic conventions. First, the preamble of “a method of preparing a personalized yeast model for determining a subject at risk of a disease” is phrased in an awkward manner. While the recited method appears to be drawn to determining whether a subject is at risk of a disease, the instant claim language may be interpreted to recite that the subject is known to be at risk of a disease and that the method claimed therein is for determining something about the subject, which is not clarified by the instant claim language. It would be remedial to amend the instant preamble such that it is clear what subject is being queried and for what purpose, for example by reciting “a method of preparing a personalized yeast model for determining whether a subject is at risk of a disease” (bolded and underlined emphasis added). This is merely an example set forth by the Examiner and is not intended to be limiting.
Regarding the body of instant claim 55, a colon separating lines two and three (following “the method comprising”) is required. Additionally, while step (b) recites that ornithine transcarbamylase is acronymized as “OTC,” step (d) recites “a homologous gene of the gene encoding O.” This appears to be a simple typographical error meant to recite “OTC.” Furthermore, the recitation of step (f) would be clearer and easier to interpret with the addition of commas separating phrases in the claim language as follows: “…wherein when test cell growth is comparable to that of the control cell, it indicates that the gene encodes a functional OTC protein, and wherein when the test cell growth is slow as compared to the control cell, it indicates that the gene encodes a non-functional OTC protein or OTC protein with decreased function” (bolded and underlined emphasis added). Finally, step (i) recites “presenting the one or more personalized disease amelioration recommendations for the first subject in the personalized yeast model for the first subject in the personalized yeast model for the first subject for disease management,” which is constructed in a confusing manner that is difficult to interpret. For purposes of examination, the Examiner has interpreted step (i) to recite “presenting the one or more personalized disease amelioration recommendations for the first subject in the personalized yeast model to the first subject for disease management” (bolded and underlined emphasis added). It would be remedial to amend the instant claim language such that it comports with standard grammatical and/or linguistic conventions, as set forth above.
Claim 56 does not comport with standard grammatical and/or linguistic conventions. Specifically, the recitation of “wherein the method further comprising” (bolded and underlined emphasis added) at lines 1-2 is grammatically improper. It would be grammatically proper to recite “wherein the method further comprises” (bolded and underlined emphasis added). Additionally, the recitation of “second set of two alleles have a second gene encoding OTC” at line 4 is grammatically improper, as it lacks a preceding article, and linguistically improper, as this recitation is awkward to one of ordinary skill in the art. It would be grammatically proper to include an article preceding the recited “second set of two alleles.” Furthermore, it would be linguistically proper to amend the instant claim language to clarify what is meant by alleles “having” a second gene, for example by reciting “the second set of two alleles corresponds to a second gene encoding OTC” (bolded and underlined emphasis added). This is merely an example set forth by the Examiner and is not intended to be limiting. Finally, there is no semicolon separating steps (a) and (b) of the method of claim 56, as is required for propriety and clarity when reciting separate steps or phrases. It would be remedial to amend the instant claim language such that it comports with standard grammatical and/or linguistic conventions, as set forth above.
Claim 58 does not comport with standard grammatical and/or linguistic conventions. The recitation of “when progeny cell growth is comparable to that of the control cell it indicates that the gene encodes a functional OTC protein, and wherein when the progeny cell growth is slow as compared to the control cell it indicates that the gene encodes a non-functional OTC protein or OTC protein with decreased function and indicates the disease” would be clearer and easier to interpret with the addition of commas separating phrases in the claim language. For example, reciting “when progeny cell growth is comparable to that of the control cell, it indicates that the gene encodes a functional OTC protein, and wherein when the progeny cell growth is slow as compared to the control cell, it indicates that the gene encodes a non-functional OTC protein or OTC protein with decreased function and indicates the disease” (bolded and underlined emphasis added) is clearer and easier to interpret. It would be remedial to amend the instant claim language such that it comports with standard grammatical and/or linguistic conventions, as set forth above.
Claim 77 does not comport with standard grammatical and/or linguistic conventions. Specifically, the recitation of “wherein a t-test p-values < 0.0001 indicates a significant growth difference” at lines 2-3 is improper. It would be remedial to amend the instant claim language such that it comports with standard grammatical and/or linguistic conventions, for example by reciting “wherein a p-value of < 0.0001 indicates a significant growth difference.” This is merely an example set forth by the Examiner and is not intended to be limiting.
Claim 78 is not structured such that it is easily and clearly interpretable by those of ordinary skill in the art. Specifically, the recitation of “the gene encodes OTC with an amino mutation otc-R141Q” is improper. One of ordinary skill in the art would be aware that a mutation named “otc-R141Q” signifies a mutation resulting in the substitution of amino acid Q (glutamine) for R (arginine). Therefore, one of ordinary skill in the art would interpret the recitation of instant claim 78 as “the gene encodes OTC with an amino acid mutation otc-R141Q” or as “the gene encodes OTC with an otc-R141Q mutation” (bolded and underlined emphasis added). In order to more easily facilitate clear interpretation by those of ordinary skill in the art, it would be remedial to amend the instant claim language, for example as set forth above. These are merely examples set forth by the Examiner and are not intended to be limiting.
Claim 79 does not comport with standard grammatical and/or linguistic conventions. Specifically, the recitation of “either the first subject is a female and the second subject is a male or the first subject is a male and the second subject is a female” lacks a comma preceding the conjunction “or” separating the first and second clauses. It would be remedial to amend the instant claim language to include a comma preceding the conjunction “or,” thereby comporting with standard grammatical and/or linguistic conventions.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(a)
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 55-58 and 70-80 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for preparing a personalized yeast model for determining whether a subject is at risk of a disease, said method comprising identifying a gene encoding ornithine transcarbamylase (OTC) in two alleles from the genomic DNA, does not reasonably provide enablement for preparing a personalized yeast model for determining whether a subject is at risk of a disease, said method comprising identifying a gene encoding ornithine transcarbamylase (OTC) in at least two alleles (i.e. more than two alleles) from the genomic DNA. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
Enablement is considered in view of the Wands factors (MPEP 2164.01(A)). These include: the breadth of the claims, the nature of the invention, the state of the prior art, the level of one of ordinary skill, the level of predictability in the art, the amount of direction provided by the inventor, the existence of working examples, and the quantity of experimentation needed to make or use the invention. All of the Wands factors have been considered with regard to the instant claims, with the most relevant factors discussed below.
Nature of the invention: Claim 55, from which claims 56-58 and 70-80 all directly or indirectly depend, is drawn to a method of preparing a personalized yeast model for determining whether a subject is at risk of a disease, said method comprising identifying a gene encoding ornithine transcarbamylase (OTC) in at least two alleles from the genomic DNA. Claims 56 and 57 additionally recite identifying a second gene of interest encoding OTC in at least two alleles from the genomic DNA obtained from a second subject. All other dependent claims do not further limit the instantly claimed “at least two alleles.” The rejected claims are thus drawn to methods of preparing a personalized yeast model for determining whether a subject is at risk of a disease, wherein the queried gene of interest (i.e. OTC) is identified in more than two alleles, as is encompassed by the instant claim language.
Breadth of the claims: As set forth above, the instant claim language encompasses identification of the queried gene of interest (i.e. OTC) in more than two alleles, with no defined upper limit of the number of identified alleles. Accordingly, the instant claim language necessarily encompasses identification of up to an unlimited number of alleles.
The complex nature of the subject matter of this invention is greatly exacerbated by the breadth of the claims.
Guidance of the specification and existence of working examples: The specification describes identification of a queried gene of interest in up to two alleles in Examples 1-4. Specifically, Example 4 discloses identification of OTC alleles. However, no description is provided of identification of a queried gene of interest in more than two alleles, as is encompassed by the instant claim language.
Predictability and state of the art: Those of ordinary skill in the art would be aware from the prior art and from the state of the field that OTC is encoded by a single gene (Magesh and Doss, 2014: page 621, column 2, paragraph 1) and that in diploid organisms such as humans, each cell carries two copies of each gene and thus, each cell carries 2 alleles of each gene (Bukaveckas et al., 2004: page 354, column 1, paragraph 3). Thus, a person of ordinary skill in the art would not reasonably predict successfully identifying more than two alleles corresponding to a single queried gene of interest (such as the OTC gene), as is encompassed by the instant claim language.
Amount of experimentation necessary: Given that those of ordinary skill in the art would not reasonably predict successfully identifying more than two alleles corresponding to a single queried gene of interest (such as the OTC gene), as is encompassed by the instant claim language, an enormous amount of experimentation would be required for the skilled artisan to disprove established biological principles in the field (see Magesh and Doss, 2014 and Bukaveckas et al., 2004-set forth above) and identify an enormous number of potential alleles corresponding to the same single gene, as the instant claim language necessarily encompasses up to an unlimited number of alleles corresponding to the same single gene.
In view of the breadth of the claims and the lack of guidance provided by the specification as well as the unpredictability of the art, the skilled artisan would have required an undue amount of experimentation to make and/or use the claimed invention. Therefore, claims 55-58 and 70-80 are not considered to be fully enabled by the instant disclosure.
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.
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 56, 57, 71, 73, and 74 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.
With regard to claim 56, which recites in part that “the second subject has a second set of two alleles that are related to the at least two alleles of the first subject, and [the] second set of two alleles…[correspond to] a second gene encoding OTC,” the Examiner has interpreted the instant claim to recite that the second set of two alleles is related to the at least two alleles of the first subject in that both sets of alleles correspond to a gene encoding OTC. However, given that the instant claim explicitly recites that the second set of two alleles corresponds to a second gene encoding OTC, it is unclear what is being claimed by reciting that the second set of two alleles is related to the at least two alleles of the first subject, as OTC is known to be encoded by a single gene (reviewed in Wilnai et al., 2018) and thus any allele corresponding to said gene must necessarily be related to each other in the sense that all of these alleles must correspond to the same gene. Thus, one of ordinary skill in the art would not be clearly apprised of the bounds of protection sought by the instant claim language. It would be remedial to amend the instant claim language to clarify what set(s) of alleles are being claimed.
Claim 57 recites the limitation "the first cell" in line 5. There is insufficient antecedent basis for this limitation in the claim. Claim 57 depends from claim 55, which recites both a test cell and a control cell. No cell in claim 55 is recited as “a first cell,” and given that both a test cell and a control cell are recited at claim 55, it is unclear whether “the first cell” of claim 57 refers to the test cell or the control cell of claim 55. For purposes of examination, the Examiner has interpreted “the first cell” of claim 57 to refer to the test cell of claim 55. It would be remedial to amend the instant claim language to clearly identify which cell is “the first cell” of claim 57.
With regard to claim 71, which recites “wherein cell growth is measured by optical density of a liquid culture, a number of pixels of a colony of cells growing on solid media,” in the absence of a coordinating conjunction such as “and” or “or” separating cell growth measurement methods, it is unclear whether cell growth should be measured by one or both methods. For purposes of examination, the Examiner has interpreted the instant claim to recite utilization of either method for measuring cell growth. It would be remedial to amend the instant claim language in order to clarify which method(s) of measurement are utilized.
With regard to claim 73, which recites that the cell growth of the test cell relative to the control cell may be measurable by “automated image analysis, wherein the test cell has an optical density…,” paragraph [0033] of the instant specification discloses that custom software for automated analysis is used to analyze and quantify cell growth on solid agar plates. However, optical density is a measure of turbidity of liquid media (see paragraph [0086] of the instant specification). It is thus unclear how one would use “automated image analysis” intended for use with cell growth on solid agar plates to determine “optical density,” which is exclusively a measure of cell growth in liquid media. For purposes of examination, the Examiner has interpreted the instant claim to require measurement and analysis of optical density measured from liquid culture rather than automated image analysis measured from growth on solid media, as the claim recites a threshold value for optical density measurements but not for automated image analysis. It would be remedial to amend the instant claim language such that the method of measurement is consistent and compatible with the method of cell growth.
With regard to claims 73 and 74, which respectively recite “the test cell has an optical density that is at least 90% of the growth value of the control cell” and that “the cell has an optical density that is 79% or less than the optical density of the control cell,” given that optical density measurements are indicative of turbidity of liquid media (see paragraph [0086] of the instant specification) resulting from the growth of multiple cells in said media, it is unclear how one would measure cell growth by measuring a single cell, as instantly recited. It would be remedial to amend the instant claim language to clarify what cell population is being measured using optical density.
Claim Rejections - 35 USC § 103
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 55, 70-72, and 77 are rejected under 35 U.S.C. 103 as being unpatentable over Hamza et al., 2015 (hereinafter Hamza; as cited in the IDS filed 11/04/2022) in view of Sun et al., 2016 (hereinafter Sun), Liu et al., 2017 (hereinafter Liu), US 2017/00617070 A1 (hereinafter Kingsmore; as cited in the IDS filed 11/04/2025), and Wilnai et al., 2018 (hereinafter Wilnai), as evidenced by Bukaveckas et al., 2004 (hereinafter Bukaveckas), Paulson, 2017 (hereinafter Paulson), and Singh, 2013 (hereinafter Singh).
With regard to claim 55, which recites “a method of preparing a personalized yeast model for determining a subject at risk of a disease, the method comprising[:]
a) obtaining genomic DNA from a first subject;
b) identifying a gene encoding ornithine transcarbamylase (OTC) in at least two alleles from the genomic DNA;
c) inserting the gene into a construct, wherein the construct is a linear DNA;
d) providing a test cell, wherein the test cell has a homologous gene of the gene encoding O[TC], wherein the homologous gene has been knocked out of the test cell;
e) introducing the construct into the test cell;
f) evaluating the test cell for cell growth in a media, wherein the media lacks an amino acid, wherein the test cell growth is compared to a control cell that has the homologous gene, wherein when test cell growth is comparable to that of the control cell[,] it indicates that the gene encodes a functional OTC protein, and wherein when the test cell growth is slow as compared to the control cell[,] it indicates that the gene encodes a non-functional OTC protein or OTC protein with decreased function and indicates the disease;
g) generating data for a look-up table;
h) generating one or more personalized disease amelioration recommendations for the first subject; and
i) presenting the one or more personalized disease amelioration recommendations for the first subject in the personalized yeast model…[to] the first subject for disease management,” both Hamza and Sun disclose the utility of testing human genes for complementation with yeast genes in order to assess genetic variants, as set forth below. Hamza discloses that model organisms such as yeast can be utilized to test human genetic variants by assaying human-yeast gene complementation pairs for growth defects (abstract). These assays include inserting a queried gene of interest into an expression vector, transforming said expression vector into a corresponding haploid-convertible heterozygous diploid knockout yeast strain (homologs are disclosed at tables S2, S3, and S5), growing the transformants in media lacking leucine, and monitoring cell growth of both mutant and wild-type yeast by measuring optical density every 30 minutes over a period of 48 hours to calculate area under the curve (AUC) value, which is a measure of cell growth (page 1265, column 2, paragraphs 1 and 2). Hamza specifically discloses that mutant alleles that result in a nonfunctional protein reduce strain fitness (page 1273, column 1, paragraph 1), wherein strain fitness is defined as the AUC (i.e. growth) of the mutant curves relative to the AUC of the wild-type allele (page 1265, column 2, paragraph 2). Thus, the disclosure of Hamza reads on steps (c)-(f) of instant claim 55, with the exception of the linear DNA construct of step (c). This deficiency is cured by Liu, which discloses that transformation of a linear DNA construct into yeast is a robust and well-established methodology (page 8, paragraph 3).
Similarly, Sun discloses that yeast-based functional complementation assays may be used to measure the impact of human disease mutations with significantly higher precision and specificity than current computational methods (abstract). Per Sun, these methods are particularly relevant to improving carrier screening and pre-implantation embryonic screening (page 670, column 1, paragraph 1). As depicted in Figure 1, Sun discloses that complementation relationships between human and yeast genes are identified by assessing whether a human gene provided in a yeast expression plasmid rescues phenotypic defects of a loss-of-function in its cognate yeast gene, said loss-of-function being generated by heterozygous diploid knockout (page 971, column 1, paragraph 3-column 2, paragraph 2; page 677, column 2, paragraphs 2 and 3), thereby facilitating the identification and characterization of deleterious pathogenic variants (page 677, column 1, paragraph 5). This rescue of the null mutant may be monitored by evaluating differences in cell growth in liquid media or on solid media (Figure 2; page 678, column 1, paragraphs 2 and 3). Sun further discloses that the data obtained from the experimentation disclosed therein may be used to provide a look-up table for functionality of human variants and to identify potential therapeutics for the queried disease mechanism/gene (page 676, column 2, paragraph 4), as in steps (g) and (h) of instant claim 55.
Regarding steps (a) and (i) of instant claim 55, Kingsmore discloses detection of nucleotide sequence variants in patients for purposes of diagnosing genetic diseases (abstract), albeit by different methodology than the human-yeast complementation assays disclosed in Hamza and Sun. The disclosure of Kingsmore establishes that diagnosis of genetic diseases in patients required extraction of genomic DNA from said patients (paragraph [0140]), as recited at step (a) of instant claim 55. Furthermore, Kingsmore discloses that all patients provided informed written consent for participating in diagnosis and treatment of genetic disease (paragraphs [0053] and [0056]). Thus, it is considered that Kingsmore discloses that for purposes of diagnosing and treating a genetic disease, the patient’s genomic DNA must be isolated in order to be studied, and the data obtained therefrom may be used to inform treatment options, as in steps (a) and (i) of instant claim 55.
Regarding step (b) of instant claim 55, Wilnai discloses that mutations in the ornithine transcarbamylase (OTC) gene cause OTC deficiency, which is a severe X-linked condition that can be diagnosed prenatally and presents particularly severely in hemizygous males (abstract; page 297, column 2, paragraph 1; page 298, column 1, paragraph 2). Bukaveckas teaches that humans are diploid organisms, wherein each cell carries two copies of each gene and thus carries two alleles of each gene (page 354, column 1, paragraph 3). Per Wilnai, a prenatal diagnosis of urea cycle defects such as OTC deficiency is essential to initiating appropriate therapy as soon as possible to offer a better outcome (page 299, column 1, paragraphs 5-6). Thus, Wilnai motivates assaying the OTC gene (of which humans have two alleles) to diagnose OTC deficiency, as in step (b) of instant claim 55.
With regard to claim 70, which recites “the personalized yeast model [of the method of claim 55] is for determining prenatal risk of the disease,” as set forth above, Sun discloses that yeast-based functional complementation assays may be used to measure the impact of human disease mutations with significantly higher precision and specificity than current computational methods, and that these assays are particularly relevant to improving carrier screening and pre-implantation embryonic screening (abstract; page 670, column 1, paragraph 1). Pre-implantation embryonic screening is performed following in vitro fertilization to select embryos generated from the process for implantation (taught in Paulson). Thus, it is considered the pre-implantation embryonic screening is used to determine prenatal disease risk. As set forth above, Wilnai discloses that early, prenatal diagnosis of OTC deficiency is essential to initiating appropriate therapy as soon as possible to offer a better outcome (page 299, column 1, paragraphs 5-6). Thus, it is considered that Sun and Wilnai collectively disclose and/or motivate each and every additional limitation of instant claim 70, as set forth in greater detail below.
With regard to claim 71, which recites “the method of claim 55, wherein cell growth is measured by optical density of a liquid culture, [or] a number of pixels of a colony of cells growing on solid media,” as set forth above, both Hamza and Sun disclose evaluating cell growth in liquid media (via optical density or absorbance at 600 nm) or on solid media (Hamza: Figures S1-S4 and page 1265, column 2, paragraph 2; Sun: Figure 2). Thus, both Hamza and Sun disclose each and every additional limitation of instant claim 71.
With regard to claim 72, which recites “the method of claim 5, wherein the evaluating step comprises measuring cell growth for 0.5, 2, 4, 6, 8, 10, 12, 24, 36, 72, 96, or 120 hours or any number of hours in between a range defined by any two aforementioned values,” as set forth above, both Hamza and Sun disclose evaluating cell growth in liquid media (via optical density or absorbance at 600 nm) or on solid media (Hamza: Figures S1-S4 and page 1265, column 2, paragraph 2; Sun: Figure 2) over periods of time including 48 hours (Hamza: page 1265, column 2, paragraph 2) and 25 hours (Sun: Figure 2), which falls within the range defined by 24 and 36 hours, as in instant claim 72. Thus, both Hamza and Sun disclose each and every additional limitation of instant claim 72.
With regard to claim 77, which recites “a t-test is performed between the test cell and control cell to determine a significant growth difference, wherein…[a p-value of] < 0.0001 indicates a significant growth difference between the test cell and control cell,” as set forth above, Hamza discloses that mutant alleles that result in a nonfunctional protein reduce strain fitness (page 1273, column 1, paragraph 1), wherein strain fitness is defined as the AUC (i.e. growth) of the mutant curves relative to the AUC of the wild-type allele (page 1265, column 2, paragraph 2). Significant differences in growth are disclosed to have been determined using a t-test (page 1265, column 2, paragraph 2). While Hamza is silent as to the significance threshold for p-values calculated from said t-test, these thresholds are generally standard in the field, as evidenced by Singh, which discloses that a p-value of less than 0.0001 is an extremely low p-value with clinical relevance, as its low value indicates that the queried results are not accidental and can be used as strong evidence against the null hypothesis (table of page 3; page 3, paragraph 8). Thus, Hamza, as evidenced by Singh, discloses each and every additional limitation of instant claim 77.
Hamza specifically discloses mutant alleles that result in a nonfunctional protein reduce strain fitness (page 1273, column 1, paragraph 1), wherein strain fitness is defined as the AUC (i.e. growth) of the mutant curves relative to the AUC of the wild-type allele (page 1265, column 2, paragraph 2).
Given that Hamza discloses that model organisms such as yeast can be utilized to test human genetic variants by comparing growth of human-yeast gene complementation pairs (generated by inserting a human gene into a yeast cell in which the corresponding gene has been knocked out) to wild-type growth using a t-test (with a p-value significance threshold of 0.0001, as taught by Singh); that Sun similarly discloses that yeast-based functional complementation assays may be used to measure the impact of human disease mutations for carrier screening and pre-implantation screening (which is used to determine prenatal disease risk per Paulson) with significantly higher precision and specificity than current computational methods and to generate a look-up table for functionality of human gene variants and to identify potential therapeutics for the queried disease mechanism/gene; that Kingsmore discloses that for purposes of diagnosing and treating a genetic disease, the patient’s genomic DNA must be isolated in order to be studied, and the data obtained therefrom may be used to inform treatment options; and that Wilnai discloses that mutations in the ornithine transcarbamylase (OTC) gene (of which humans have two alleles per Bukaveckas) cause OTC deficiency, which is a severe X-linked condition that can be diagnosed prenatally and presents particularly severely in hemizygous males, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to diagnose and treat genetic diseases (as disclosed in Kingsmore) using the methodology disclosed by Hamza and Sun to detect mutations in the OTC gene to predictably determine carrier status or prenatal risk of developing OTC deficiency due to a mutated, non-functional OTC gene. One would have been motivated to make such a modification in order to receive the expected benefit of identifying OTC deficiency mutations with significantly higher precision and specificity than current computational methods, thereby facilitating treatment (including prenatal treatment) to offer better outcomes for affected patients.
Claims 56, 79, and 80 are rejected under 35 U.S.C. 103 as being unpatentable over Hamza et al., 2015 (hereinafter Hamza; as cited in the IDS filed 11/04/2022) in view of Sun et al., 2016 (hereinafter Sun), Liu et al., 2017 (hereinafter Liu), US 2017/00617070 A1 (hereinafter Kingsmore; as cited in the IDS filed 11/04/2025), and Wilnai et al., 2018 (hereinafter Wilnai), as evidenced by Bukaveckas et al., 2004 (hereinafter Bukaveckas), Paulson, 2017 (hereinafter Paulson), and Singh, 2013 (hereinafter Singh) as applied to claim 55 above, and further in view of Wadsworth Center Prenatal Genetics Referrals, 2019 (hereinafter Wadsworth).
The combined disclosures of Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, Paulson, and Singh are described above and applied as before. However, these disclosures do not teach the second subject of instant claim 56, the prenatal testing of instant claim 70, or the subjects of instant claims 79 and 80.
With regard to claim 56, which recites “the method of claim 55…further compris[es]: a) obtaining a second genomic DNA from a second subject, wherein the second subject has a second set of two alleles that are related to the at least two alleles of the first subject, and [the] second set of two alleles” corresponds to “a second gene encoding OTC, wherein the second gene encoding OTC is placed in a second construct; b) introducing the second construct into a second test cell, evaluating the second test cell for cell growth in a media, wherein the media lacks an amino acid, wherein the test cell growth is compared to a control cell that has the homologous gene, wherein when second test cell growth is comparable to that of the control cell[,] it indicates that the gene encodes a functional OTC protein and wherein the test cell growth is slow as compared to the control cell[,] it indicates that the gene encodes a non-functional OTC protein or OTC protein with decreased function,” as set forth above, both Hamza and Sun disclose human-yeast complementation assays in which the ability of a human gene to rescue a null mutant of the corresponding yeast homolog is determined by introducing a construct carrying said human gene into a haploid yeast strain in which the corresponding homolog is knocked out and subsequently monitoring growth of mutant and control cells (see sections cited above regarding instant claim 55). Sun discloses that yeast-based functional complementation assays may be used to measure the impact of human disease mutations with significantly higher precision and specificity than current computational methods, and that these assays are particularly relevant to improving carrier screening and pre-implantation embryonic screening (abstract; page 670, column 1, paragraph 1). Additionally, as set forth above, Wilnai discloses that mutations in the ornithine transcarbamylase (OTC) gene (of which humans have two alleles per Bukaveckas (page 354, column 1, paragraph 3)) cause OTC deficiency, which is a severe X-linked condition that presents particularly severely in hemizygous males and can be diagnosed prenatally to improve treatment outcomes (abstract; page 297, column 2, paragraph 1; page 298, column 1, paragraph 2; page 299, column 1, paragraphs 5-6). While none of the cited art discloses testing a second subject, this deficiency is cured by Wadsworth.
Wadsworth discloses that carrier screening can be performed at any time before or during pregnancy, wherein genetic testing is performed in one or both parents in order to determine risk for a child conceived to be affected with recessive or x-linked genetic conditions (table 1 on page 2). As set forth above, Wilnai discloses that OTC deficiency is a severe X-linked condition (abstract). Accordingly, in view of the disclosure of Wadsworth, carrier testing for OTC deficiency would be indicated in one or both parents (i.e. first and second subjects) in order to determine risk for their child to be affected with OTC deficiency, as it is a severe X-linked condition. As set forth above, the method collectively disclosed by Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, and Singh comprises introducing the queried gene into a construct that is then transformed into a knockout yeast test cell and evaluating growth of the test and control cells, as instantly claimed. Furthermore, as set forth above regarding instant claim 70, the disclosure of Sun explicitly teaches that human-yeast gene complementation testing is well-suited to carrier screening (as disclosed in Wadsworth) and pre-implantation embryonic screening (abstract; page 670, column 1, paragraph 1). Thus, it is considered that Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, Paulson, Singh, and Wadsworth collectively disclose the method of claim 56.
With regard to claim 79, which recites “either the first subject [of the method of claim 56] is a female and the second subject is a male[,] or the first subject is a male and the second subject is a female,” as set forth above, Wadsworth discloses that carrier screening of both parents can be performed at any time before or during pregnancy to determine the risk for a child conceived to be affected with recessive or x-linked genetic conditions (table 1 on page 2), such as OTC deficiency (Wilnai: abstract). Given that carrier screening is indicated in both parents to determine the risk of their child inheriting an x-linked genetic condition, and that genetically, one parent must be male and one parent must be female, it is considered that the two subjects of the method of instant claim 56 must be male and female, as instantly claimed. Thus, it is considered that Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, Paulson, Singh, and Wadsworth collectively disclose the subject matter of claim 79.
With regard to claim 80, which recites “when the subject [of the method of claim 79] is female, the subject is pregnant,” as set forth above, Wadsworth discloses that carrier screening of both parents can be performed at any time before or during pregnancy to determine the risk for a child conceived to be affected with recessive or x-linked genetic conditions (table 1 on page 2), such as OTC deficiency (Wilnai: abstract). Given that carrier screening is indicated at any time before or during pregnancy, it is considered that such screening is indicated in pregnant female subjects, as instantly claimed. Thus, it is considered that Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, Paulson, Singh, and Wadsworth collectively disclose the subject matter of claim 80.
Given that Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, Paulson, and Singh collectively disclose a method of preparing a personalized yeast model for determining a subject at risk of a disease as recited at instant claim 55, wherein Sun explicitly discloses that human-yeast gene complementation testing is well-suited to carrier screening and pre-implantation embryonic screening, and that Wadsworth discloses that carrier screening can be performed in one or both parents at any time before or during pregnancy in order to determine risk for a child conceived to be affected with x-linked genetic conditions (such as OTC deficiency, as disclosed in Wilnai), it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to utilize the method collectively disclosed by Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, Paulson, and Singh to perform carrier screening in both parents, before or during pregnancy, to predictably determine the risk of a child conceived by said couple being affected with an x-linked genetic condition such as OTC deficiency. One would have been motivated to make such a modification in order to receive the expected benefit of precisely and specifically identifying disease risk via carrier screening performed with human-yeast gene complementation (as disclosed in Sun).
Claims 57, 58, 73, and 74 are rejected under 35 U.S.C. 103 as being unpatentable over Hamza et al., 2015 (hereinafter Hamza; as cited in the IDS filed 11/04/2022) in view of Sun et al., 2016 (hereinafter Sun), Liu et al., 2017 (hereinafter Liu), US 2017/00617070 A1 (hereinafter Kingsmore; as cited in the IDS filed 11/04/2025), and Wilnai et al., 2018 (hereinafter Wilnai), as evidenced by Bukaveckas et al., 2004 (hereinafter Bukaveckas), Paulson, 2017 (hereinafter Paulson), and Singh, 2013 (hereinafter Singh) as applied to claim 55 above, and further in view of Wadsworth Center Prenatal Genetics Referrals, 2019 (hereinafter Wadsworth) and Trevisson et al., 2009 (hereinafter Trevisson; as cited in the IDS filed 11/04/2022).
The combined disclosures of Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, Paulson, and Singh are described above and applied as before. However, these disclosures do not teach the cell mating of instant claim 57 or the media of instant claim 58.
With regard to claim 57, which recites “the method of claim 55 further compris[es] obtaining a second genomic DNA from a second subject and identifying a second gene(s) of interest encoding OTC in at least two alleles from the genomic DNA, inserting at least one of the second gene(s) of interest encoding OTC into a second construct, introducing the second construct into a second test cell, and mating the second cell with the first cell to produce a progeny cell,” as set forth above regarding instant claim 56, Wadsworth discloses that carrier screening can be performed at any time before or during pregnancy, wherein genetic testing is performed in one or both parents in order to determine risk for a child conceived to be affected with x-linked genetic conditions (table 1 on page 2), such as OTC deficiency (Wilnai: abstract). Given that Sun discloses that human-yeast complementation assays are highly accurate and particularly useful for carrier screening (abstract; page 670, column 1, paragraph 1), it is considered that it would have been obvious to someone of ordinary skill in the art prior to the effective filing date of the claimed invention to utilize the method collectively disclosed by Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, Paulson, and Singh to perform carrier screening in both parents (i.e. two subjects), before or during pregnancy, to predictably determine the risk of a child conceived by said couple being affected with an x-linked genetic condition such as OTC deficiency, as set forth in greater detail above regarding instant claim 70. However, the cited art set forth above is silent as to the production of a progeny cell by mating two test cells.
This deficiency is cured by Trevisson. Trevisson discloses yeast-based functional complementation assays to assess the pathogenicity of mutations in argininosuccinate lyase (ASL) that cause argininosuccinic aciduria, which is a urea cycle defect (abstract). It is noted that OTC deficiency is also a urea cycle defect (Wilnai: abstract) and that Trevisson discloses that the methods taught therein may be easily adapted for the analysis of mutations in other genes involved in urea cycle disorders (abstract). The methods of Trevisson 2009 producing transformant yeast by transforming haploid yeast cells lacking the yeast homolog of the human ASL gene with constructs comprising human and yeast ASL or ARG4 sequences and monitoring the ability of cells to grow on media lacking arginine (page 28928, column 1, paragraphs 2 and 3). Furthermore, Trevisson further discloses mating said transformants to produce diploid, “compound heterozygous” yeast to monitor their growth on media lacking arginine as a readout for intragenic complementation (abstract; page 28928, column 2, paragraphs 3 and 4; Figures 4 and 5). Thus, it is considered that Trevisson discloses each and every additional limitation of instant claim 57 not addressed above.
With regard to claim 58, which recites “the method of claim 57 further compris[es] evaluating the progeny cell for cell growth in a media, wherein the media lacks arginine, wherein the test cell growth is compared to a control cell that has the homologous gene, wherein when progeny cell growth is comparable to that of the control cell[,] it indicates that the gene encodes a functional OTC protein, and wherein when the progeny cell growth is slow as compared to the control cell[,] it indicates that the gene encodes a non-functional OTC protein or OTC protein with decreased function and indicates the disease,” as set forth above, Trevisson discloses mating yeast transformants and monitoring their growth on media lacking arginine, wherein growth on media lacking arginine is indicative of functional complementation (page 28928, column 2, paragraph 1; page 28928, column 2, paragraph 3). Furthermore, Wilnai discloses that administration of arginine to subjects with OTC deficiency is therapeutic, as the biochemical hallmarks of OTCD include low levels of arginine, the administration of which activates alternative pathways of nitrogen elimination (abstract; page 298, column 1, paragraphs 1 and 3). Thus, one of ordinary skill in the art would reasonably expect that media lacking arginine would not be able to rescue the growth of cells modeling OTC deficiency. Accordingly, it is considered that Trevisson, in view of Wilnai, discloses each and every additional limitation of instant claim 58.
With regard to claims 73 and 74, which respectively recite “wherein cell growth of the test cell is comparable to that of the control cell…the test cell [of the method of claim 55] has an optical density that is at least 90% of the growth value of the control cell,” and that “wherein cell growth of the test cell [of the method of claim 55] is slow as compared to the control cell, wherein the cell has an optical density that is 79% or less than the optical density of the control cell,” these claims have been interpreted as set forth in section Claim Rejections - 35 USC § 112(b). As set forth above, it is considered that Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, Paulson, and Singh collectively disclose the method of instant claim 55. Furthermore, Trevisson depicts the growth of mutant and control yeast transformed by the methods set forth above in Figure 2. While the growth depicted in Figure 2 is done on solid media, the Examiner notes that the instant claim language does not require measurement of optical density. The instant claim language merely requires that the optical density of the test and control cells be compared, with threshold values of greater than 90% indicating lack of disease state and less than 79% indicating disease state. As shown in Figure 2 of Trevisson, the mutants in the left image do not show any significant growth on solid media as compared to the control cells, meaning a measurement of their optical density would reasonably be expected to be less than 79% of the value of the optical density of the control cells, thereby indicating the disease state (see also page 28928, column 2, paragraph 3). The mutants in the right image, however, do show retention of residual growth in certain alleles such that a measurement of their optical density would reasonably be expected to be greater than 90% of the value of the optical density of the control cells, thereby indicating lack of the disease state (see also page 28928, column 2, paragraph 3). Thus, it is considered that Trevisson discloses each and every additional limitation of instant claims 73 and 74.
Given that Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, Paulson, and Singh collectively disclose a method of preparing a personalized yeast model for determining a subject at risk of a disease as recited at instant claim 55, that Wilnai specifically discloses that OTC deficiency is a urea cycle defect that can be treated (in part) by administering arginine to compensate for low levels of arginine in affected subjects and activate alternative pathways of nitrogen elimination, and that Trevisson discloses production of diploid, “compound heterozygous” yeast to assay growth on media lacking arginine as a readout for intragenic complementation of another gene implicated in a urea cycle defect, wherein lack of growth of test cells as compared to control cells indicates the disease state and retention of growth of test cells as compared to control cells indicates lack of the disease state, it would have been obvious to someone of ordinary skill in the art prior to the effective filing date of the claimed invention to mate the haploid yeast produced from subjects 1 and 2 (i.e. the parents) using the method collectively disclosed by Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, Paulson, and Singh to generate a diploid, “compound heterozygous” yeast to assay growth on media lacking arginine as a readout for intragenic complementation (as in Trevisson) to predictably detect intragenic complementation, wherein growth on media lacking arginine is indicative of functional complementation (as disclosed in Trevisson). One would have been motivated to make such a modification in order to receive the expected benefit of precisely and specifically identifying disease risk of a child produced by subjects 1 and 2 (i.e. the parents) via screening performed with human-yeast gene complementation (as disclosed in Sun).
Claims 75, 76, and 78 are rejected under 35 U.S.C. 103 as being unpatentable over Hamza et al., 2015 (hereinafter Hamza; as cited in the IDS filed 11/04/2022) in view of Sun et al., 2016 (hereinafter Sun), Liu et al., 2017 (hereinafter Liu), US 2017/00617070 A1 (hereinafter Kingsmore; as cited in the IDS filed 11/04/2025), and Wilnai et al., 2018 (hereinafter Wilnai), as evidenced by Bukaveckas et al., 2004 (hereinafter Bukaveckas), Paulson, 2017 (hereinafter Paulson), and Singh, 2013 (hereinafter Singh) as applied to claim 55 above, and further in view of Magesh and Doss, 2014 (hereinafter Magesh).
The combined disclosures of Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, Paulson, and Singh are described above and applied as before. However, these disclosures do not teach the single-nucleotide polymorphism of instant claims 75 and 76 or the specific OTC mutation of instant claim 78.
With regard to claim 75, which recites “the gene [of the method of claim 55] is further analyzed for a single-nucleotide polymorphism,” as set forth above, it is considered that Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, Paulson, and Singh collectively disclose the method of instant claim 55. Additionally, Kingsmore discloses that single-nucleotide polymorphisms (SNPs) are useful in calling variants during sequencing (paragraph [0036]) and can in fact indicate known disease variants (paragraph [0127]). Furthermore, Magesh discloses that the variants of the OTC gene are known to comprise mutations that are deleterious SNPs causing OTC deficiency (abstract). Thus, it is considered that Kingsmore and Magesh disclose each and every additional limitation of instant claim 75.
With regard to claim 76, which recites “the single-nucleotide polymorphism [of the method of claim 75] is identified as being associated with loss of function or decreased function of OTC protein encoded by the gene,” as set forth above, Magesh discloses that the variants of the OTC gene are known to comprise mutations that are deleterious SNPs causing OTC deficiency (abstract). Thus, it is considered that Magesh discloses each and every additional limitation of instant claim 76.
With regard to claim 78, which recites “the gene [of the method of claim 55] encodes OTC with an amino [acid] mutation otc-R141Q,” as set forth above, Magesh discloses that the variants of the OTC gene are known to comprise mutations that are deleterious SNPs causing OTC deficiency (abstract). One such disease-causing SNP is disclosed to be the R141Q mutation, in which Q (glutamine) is substituted for R (arginine), thereby altering OTC protein structure and decreasing its stability (Tables 1, 2, and 5). Thus, it is considered that Magesh discloses each and every additional limitation of instant claim 78.
Given that Hamza, Sun, Liu, Kingsmore, Wilnai, Bukaveckas, Paulson, and Singh collectively disclose a method of preparing a personalized yeast model for determining a subject at risk of a disease as recited at instant claim 55, that Kingsmore explicitly discloses detecting SNPs as part of a workflow for diagnosing genetic diseases, and that Magesh discloses that the R141Q mutation in the OTC gene is a disease-causing SNP that alters OTC protein structure and decreases its stability, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to further analyze the OTC gene of the subject of the method of claim 55 to predictably determine whether said OTC gene comprises disease-causing SNPs such as the R141Q mutation. One would have been motivated to make such a modification in order to receive the expected benefit of assessing the queried subject for deleterious SNPs such as the R141Q mutation in the OTC gene.
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).
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Claims 55, 70-78, and 80 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3 and 5-13 of copending Application No. 17/047,667 (corresponds to US 2021/0155971 A1; as cited in the IDS filed 11/04/2022) in view of Sun et al., 2016 (hereinafter Sun), Wilnai et al., 2018 (hereinafter Wilnai), US 2017/00617070 A1 (hereinafter Kingsmore; as cited in the IDS filed 11/04/2025), and Magesh and Doss, 2014 (hereinafter Magesh).
Copending claim 1 recites a method of screening a subject for a disease associated with an amino acid deficiency, said method comprising obtaining genomic DNA from the subject, identifying a gene of interest from the genomic DNA (wherein the subject is determined to have a variant of the gene of interest), inserting the variant of the gene of interest into a linear DNA construct that is introduced into a test cell (limited to a yeast cell at copending claim 3) wherein the homologous gene of the variant gene of interest has been knocked out of the test cell, and evaluating the test cell for cell growth via a yeast cell assay in a media lacking an amino acid. Copending claim 1 further recites that when test cell growth is lower than that of a control cell (limited to a yeast cell at copending claim 3) comprising the homologous gene knocked out in the test cell, it is indicative that the gene variant encodes a non-functional protein or protein with decreased function. Copending claim 1 further recites that the quantified growth of the test cell is compared with quantified growth information recorded in a look-up table of other variants, thereby identifying the subject as having the disease when quantified growth of the test cell with the variant in the yeast cell assay is comparable to or lower than the predicted threshold. Copending claim 6 limits the gene of interest assessed via the method of copending claim 1 to a gene encoding 3-PGDH, PSAT1, or PSPH.
The limitations recited at copending claims 1 and 3 collectively read on each and every limitation recited at instant claim 55, with the exception of the gene of interest being OTC (and the associated disease being OTC deficiency), generating data for a look-up table, generating personalized disease amelioration recommendations, and presenting said recommendations to the subject. However, these deficiencies are cured by various secondary references. Wilnai discloses that mutations in the OTC gene cause OTC deficiency, which is a severe X-linked condition that can be diagnosed prenatally and presents particularly severely in hemizygous males (abstract; page 297, column 2, paragraph 1; page 298, column 1, paragraph 2). Per Wilnai, a prenatal diagnosis of urea cycle defects such as OTC deficiency is essential to initiating appropriate therapy as soon as possible to offer a better outcome (page 299, column 1, paragraphs 5-6). Thus, while copending claim 6 limits the gene of interest to a gene encoding 3-PGDH, PSAT1, or PSPH, the disclosure of Wilnai motivates utilizing the same method for assaying the OTC gene to diagnose OTC deficiency, as in instant claim 55.
Additionally, Sun discloses that data obtained from human-yeast complementation assays may be used to generate a look-up table of human disease variants before they have even been observed in the clinic (page 676, column 2, paragraph 4). Furthermore, Kingsmore discloses that all patients provided informed written consent for participating in diagnosis and treatment of genetic disease (paragraphs [0053] and [0056]). Thus, it is considered that Kingsmore discloses that for purposes of diagnosing and treating a genetic disease, the data obtained from testing for such diseases (i.e. by the methods of the instant and copending applications) may be used to inform patients of treatment options for their specific genetic disease.
Copending claim 2 limits the subject to be screened by the method of claim 1 to a fetus, a neonate, juvenile, or adult, while copending claim 5 limits the subject to be screened by the method of claim 1 to a pregnant person.
The limitations recited at copending claims 2 and 5 are not patentably distinct from the limitations recited at instant claims 70 and 80, which respectively recite that the claimed method is used to determine prenatal risk of disease, and that the tested subject is a pregnant female. Regarding the claimed determination of prenatal risk of disease, assessing a fetus via the methods of the instant and copending applications would necessarily have the effect of determining prenatal risk of disease. Additionally, a subject that is a pregnant adult reads on all limitations of copending claims 2 and 5, as well as of instant claim 80.
Copending claim 7 recites that measuring the area of the spot of the test cell growing on solid media comprises determining a number of pixels of the area, which is identical to the limitations recited at instant claim 71 regarding measurement of growth on solid media.
Copending claim 8 recites that evaluation of cell growth comprises measuring cell growth for 0.5, 2, 4, 6, 8, 10, 12, 24, 36, 72, 96, or 120 hours or any number of hours in between a range defined by any two of the aforementioned values, which is identical to the limitations recited at instant claim 72.
Copending claims 9 and 10 recite that when quantified growth of the test cell is comparable to the quantified growth of the control cell, the test cell has at least 90% of a growth value of the control cell, while when quantified growth of the test cell is lower to the quantified growth of the control cell, the test cell has less than 79% of a growth value of the control cell. This is identical to the limitations recited at instant claims 73 and 74. Although instant claims 73 and 74 recite that optical density is the queried growth value, the broadly claimed, generic “growth value” of copending claims 9 and 10 reads on the optical density of instant claims 73 and 74. This is supported by the disclosure of Sun, which discloses measuring optical density to assess cell growth (Figure 2).
Copending claims 11 and 12 recite that the variant of the gene of interest of the method claimed therein is further analyzed for a single-nucleotide polymorphism, said single-nucleotide polymorphism being limited to being associated with the non-functional protein or protein with decreased function. These limitations are identical to the limitations recited at instant claims 75 and 76, with the exception of the gene of interest of the instant application (OTC). However, as set forth above, Wilnai motivates utilizing the methods of both the instant and copending applications for assaying the OTC gene to diagnose OTC deficiency. Additionally, Magesh discloses that the variants of the OTC gene are known to comprise mutations that are deleterious SNPs causing OTC deficiency (abstract). One such disease-causing SNP is disclosed to be the R141Q mutation, in which Q (glutamine) is substituted for R (arginine), thereby altering OTC protein structure and decreasing its stability (Tables 1, 2, and 5). This mutation is recited at instant claim 78.
Copending claim 13 recites that quantified growth of the test cell and of the control cell is compared using a t-test, wherein a t-test with a p-value of < 0.0001 indicates a significant growth difference between the quantified growth of the test cell and of the control cell, which is identical to the limitations recited at instant claim 77.
Thus, the copending application discloses a method of assessing gene variants of a gene of interest in subjects such as fetuses and pregnant subjects using yeast cells, wherein the methodology of the copending application reads on each and every limitation of the instantly claimed methodology, with the exception of the queried gene of interest, the generation of a look-up table, and informing the subject of their personalized treatment plan, all of which are addressed by various secondary references, as set forth above. Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to select OTC as the gene of interest (as motivated by Wilnai) to be assessed for variants and incorporated into a genetic variant look-up table (as disclosed in Sun) in order to inform patients of treatment options for their specific genetic disease (as disclosed in Kingsmore) to predictably detect and assess variant OTC sequences and provide appropriate treatment as early as possible (as disclosed in Wilnai and set forth above). One would have been motivated to make such a modification in order to receive the expected benefit of detecting and assessing variant OTC sequences and providing appropriate treatment as early as possible.
This is a provisional nonstatutory double patenting rejection.
Conclusion
No claims are allowed.
Claims 55, 56, 58, and 77-79 are objected to.
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/SARAH E ALLEN/ Examiner, Art Unit 1637
/J. E. ANGELL/ Primary Examiner, Art Unit 1637