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 .
The claims filed 12/9/2022 are under consideration.
Examiner’s Note
The applicant for the present application is “Affymetric, Inc.”. The applicant for the parent application 16/616,725 is “Affymetrix, Inc.”. The oath in the present case lists the mailing address for the inventors as “Affymetrix, Inc.” and the ADS lists “Affymetric, Inc.”.
Applicant is requested to clarify on the record who the correct applicant is.
Information Disclosure Statement
The listing of references in the specification or cited throughout the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892 or cited on a submitted IDS, they have not been considered.
Claim Objections
Claim 14 is objected to because of the following informalities: the claim recites “cop number” rather than “copy number”. Appropriate correction is required.
Claim Interpretation
Independent claims 1 and 13 are drawn to a “systems”. The specification recites a “system” wherein the “system” is defined in terms of structural limitations (e.g., para. 67). In addition, the independent claims recite structural limitations of the “system”, e.g., probe microarray, etc. Thus, the “system” is interpreted to encompass any collection of structures used together that are not necessarily part of a completely integrated single unitary device. Any further interpretation of the word is considered an “intended use” and does not impart any further structural limitation on the claimed subject matter.
Claim 2 recites “the executable instructions” in line 1. The recitation is interpreted as referring to the “instructions” encoded on the memory of the computer.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-20 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.
Regarding claim 1, the claim is incomplete because there is no element that links signals specifically to a maternal or fetal genotype. Such an element is required for the instructions to be able to cause the computer to determine a copy number of a chromosome for a fetus, a fetal genotype, a maternal genotype or the fetal fraction of a sample.
Claims 2-12 depend from claim 1 and are rejected for the same reason.
Regarding claim 3, the claim is incomplete because no element in the system is identified as differentiating a fetal portion of a sample from a maternal portion of a sample.
Regarding claim 4, it is unclear what additional structural features are required by the system, if any, in order to confer the ability of first and second signals to indicate an amount of their respective alleles that are present.
Regarding claim 7, the claim recites “the first assay”, which lacks proper antecedent basis as no “first assay” is set forth or more broadly, no type of “assay” is set forth.
Regarding claim 7, the claim recites “the first maternal SNP genotype”, which lacks proper antecedent basis as no “first maternal SNP genotype” is described.
Regarding claim 7, the claim recites “the polymorphic site of the SNP”, which lacks proper antecedent basis as no “SNP” is previously set forth.
Regarding claim 13, the claim is incomplete because there is no element that links signals specifically to a minor population and/or a major population. Such an element is required for the instructions to be able to cause the computer to determine the copy number of the target chromosome in the minor population.
Claims 14-20 depend from the claim 13 and are rejected for the same reason.
Regarding claim 14, the claim is incomplete because there is no element that links signals specifically to a major population and/or a minor population. Such an element is required for the instructions to be able to cause the computer to determine the copy number of the target chromosome in a major population.
Regarding claim 15, the claim is incomplete because there is no element that links signals specifically to a major population and/or a minor population. Such an element is required for the instructions to be able to cause the computer to determine the genotype of for the minor population.
Regarding claim 16, the claim is incomplete because there is no element that links signals specifically to a major population and/or a minor population. Such an element is required for the instructions to be able to cause the computer to determine the genotype for the major population.
Regarding claim 17, the claim is incomplete because there is no element that links signals specifically to a major population and/or a minor population. Such an element is required for the instructions to be able to cause the computer to determine the relative amounts of the major and minor subpopulations.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement.
The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims encompass all “instruction” forms and structures that perform the various recited functions in the claims, e.g., determine a copy number of the target chromosome in a fetus, determine using the first signal and second signal data a fetal genotype for the SNP, determine using the first signal and second signal data a maternal genotype for the SNP, etc. The instant specification does not adequately support the full scope of the claims.
Specific programs are described that rely on particular elements and data in the computer in order make various calculations and determinations. No guidance is provided as to how one is to make such determinations and calculations without those elements and/or data. No guidance is provided to as to how to use signals to directly make any determinations. The signal data must be processed in order to make the determinations in view of the specification.
Regarding issues of written description support stemming even from the original claims and original disclosure, MPEP 2161.01.I (e.g. 6th para.), 2163.I and 2163.I.A pertain: "[O]riginal claims may lack written description when the claims define the invention in functional language specifying a desired result but the specification does not sufficiently describe how the function is performed or the result is achieved. For instructions, this can occur when the algorithm or steps/procedure for performing the computer function are not explained at all or are not explained in sufficient detail (simply restating the function recited in the claim is not necessarily sufficient). In other words, the algorithm or steps/procedure taken to perform the function must be described with sufficient detail so that one of ordinary skill in the art would understand how the inventor intended the function to be performed" (MPEP 2161.01.I,6th para.).
As noted above, specific processes for making calculations and determinations are described in the specification. These limited number of species do not adequately support the full scope of the generic calculations and determinations that the computer is caused to performed.
Claim Rejections - 35 USC § 112
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.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], 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 7-12 and 18-20 rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, 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.
Regarding claim 7, the claim describes an assay regarding how the second value is obtained. The claim does not further limit any structural element required by the system of claim 6.
Regarding claim 8, the claim fails to further limit the scope of claim 1 because it further describes an element that is not a structural feature of the claimed system. The scope of the structural features of the probe microarray, scanner and computer are not further limited by claim 8.
Regarding claim 9, the claim fails to further limit the scope of claim 7 because it further describes an element that is not a structural feature of the claimed system.
Regarding claim 10, the claim fails to further limit the scope of claim 7 because it further describes an element that is not a structural feature of the claimed system.
Regarding claim 11, the claim fails to further limit the scope of claim 7 because it further describes an element that is not a structural feature of the claimed system. The scope of the structural features of the probe microarray, scanner and computer are not further limited by claim 11.
Regarding claim 12, the claim fails to further limit the scope of claim 1 because it further describes an element that is not a structural feature of the claimed system. The scope of the structural features of the probe microarray, scanner and computer are not further limited by claim 12.
Regarding claim 18, the claim fails to further limit the scope of claim 13 because it further describes an element that is not a structural feature of the claimed system. The scope of the structural features of the probe microarray, scanner and computer are not further limited by claim 18.
Regarding claims 19 and 20, the claims fail to further limit the scope of claim 13 because they further describe an element that is not a structural feature of the claimed system. The scope of the structural features of the probe microarray, scanner and computer are not further limited by claims 19 and 20.
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 § 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(s) 1, 4-13, 15 and 18-20 is/are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Deng (WO 2010/085815 A1).
Regarding claims 1 and 4, Deng teaches a probe microarray in the form of a bead array (para. 219). The bead array comprise a plurality of probes that hybridize with a target chromosome, where a set of probes includes allele-specific oligos that are specific for each of the two alleles at a SNP (para. 220).
The bead array generates first and second signals, where one signal is associated with one allele and the other signal is associated with the other allele and the ratio of the signals determines the relative amounts of each allele (para. 220-221).
The bead array is used with a scanner in the form of the BeadArray Reader™ that detects the first and second signals separately (para. 223).
The BeadArray Reader™ is communicatively coupled to a computer having a computer program to receive the first and second signal data and to automate genotyping clusters and callings (para. 224).
The program for genotyping clusters and callings has the ability to genotype a fetal SNP and/or genotype a maternal SNP.
See also Figure 7.
Regarding claim 5, the claim does not specify the instructions cause the computer to determine a copy number of the target chromosome in a fetus, but rather limits those embodiments of claim 1 that do. Claim 5 broadly encompasses instructions that cause the computer to determine genotypes of a SNP, and Deng anticipates those embodiments.
Regarding claims 6, 7, 8, 9, 10 and 11, the claims further limit the embodiment regarding how a copy number of the target chromosome is determined. The claims broadly encompasses instructions that cause the computer to determine genotypes of a SNP, and Deng anticipates those embodiments of claims 6-11.
Regarding claim 12, the claim further limits the nucleic acid sample, which is not a structural element required by the claimed system. Deng anticipates claim 12 because it teaches all of the structural elements required by claim 12.
Regarding claims 13 and 15, Deng teaches a probe microarray in the form of a bead array (para. 219). The bead array comprise a plurality of probes that hybridize with a target chromosome, where a set of probes includes allele-specific oligos that are specific for each of the two alleles at a SNP (para. 220).
The bead array generates first and second signals, where one signal is associated with one allele and the other signal is associated with the other allele and the ratio of the signals determines the relative amounts of each allele (para. 220-221).
The bead array is used with a scanner in the form of the BeadArray Reader™ that detects the first and second signals separately (para. 223).
The BeadArray Reader™ is communicatively coupled to a computer having a computer program to receive the first and second signal data and to automate genotyping clusters and callings (para. 224).
Deng further teaches the computer is used to estimate copy number based on hybridization intensity (para. 210) and the detection of aneuploidies based on SNP detection (para. 30 and 364).
Regarding claim 18, the claim further limits the major and minor subpopulations, which are not a structural element required by the claimed system. Deng anticipates claim 18 because it teaches all of the structural elements required by claim 18.
Regarding claims 19 and 20, the claims further limit the mixed nucleic acid population, which is not a structural element required by the claimed system. Deng anticipates claims 19 and 20 because it teaches all of the structural elements required by claims 19 and 20.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 2-3, 14 and 16-17 is/are rejected under 35 U.S.C. 103 as being unpatentable over Deng (WO 2010/085815 A1) in view of Srinivisan (US 2016/0017412 A1).
Regarding claims 2 and 3, Deng teaches a probe microarray in the form of a bead array (para. 219). The bead array comprise a plurality of probes that hybridize with a target chromosome, where a set of probes includes allele-specific oligos that are specific for each of the two alleles of a SNP (para. 220).
The bead array generates first and second signals, where one signal is associated with one allele and the other signal is associated with the other allele and the ratio of the signals determines the relative amounts of each allele (para. 220-221).
The bead array is used with a scanner in the form of the BeadArray Reader™ that detects the first and second signals separately (para. 223).
The BeadArray Reader™ is communicatively coupled to a computer having a computer program to receive the first and second signal data and to automate genotyping clusters and callings (para. 224).
The program for genotyping clusters and callings has the ability to genotype a fetal SNP and/or genotype a maternal SNP.
See also Figure 7.
Regarding claim 14, 16 and 17, Deng teaches a probe microarray in the form of a bead array (para. 219). The bead array comprise a plurality of probes that hybridize with a target chromosome, where a set of probes includes allele-specific oligos that are specific for each of the two alleles at a SNP (para. 220).
The bead array generates first and second signals, where one signal is associated with one allele and the other signal is associated with the other allele and the ratio of the signals determines the relative amounts of each allele (para. 220-221).
The bead array is used with a scanner in the form of the BeadArray Reader™ that detects the first and second signals separately (para. 223).
The BeadArray Reader™ is communicatively coupled to a computer having a computer program to receive the first and second signal data and to automate genotyping clusters and callings (para. 224).
Deng further teaches the computer is used to estimate copy number based on hybridization intensity (para. 210) and the detection of aneuploidies based on SNP detection (para. 30 and 364).
Deng does not teach the elements specifically recited in claims 2, 3, 14, 16 and 17.
However, Srinivisan teaches analyses related to the genotyping of samples.
Regarding claims 2 and 3, Srinivisan teaches analyses using allele-frequencies to determine fetal fraction using genotyping data (para. 276-277).
Regarding claims 14, 16, and 17, Srinivisan teaches analyses determining the genotype and allele frequencies for a major population from a mother and a minor population from a fetus (para. 277).
It would have been prima facie obvious to the ordinary artisan to have modified the system of Deng such that is also calculate BAF, fetal frequencies the genotypes of major and minor populations of nucleic acids. One would have been motivated to do so because the programs are useful in analyzing nucleic acid samples comprising multiple sources of nucleic acids.
Conclusion
No claims allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH G DAUNER whose telephone number is (571)270-3574. The examiner can normally be reached 7 am EST to 4:30 EST with second Fridays Off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached at 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JOSEPH G. DAUNER/Primary Examiner, Art Unit 1682