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 .
Summary
1. Claims 2-20 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 the genus, does not reasonably provide enablement for the species. 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 use the invention commensurate in scope with these claims.
2. Claims 2-20 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.
3. Claims 7, 8, 12 and 13 are 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.
4. Claim 2 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,462,298.
Claim Objections
The claims are objected to because, inter alia, this claim set still includes the unwritten-out GC-LOESS acronym in claim 15 which was previously objected to by the Office in the prosecution of this family. Please carefully review the claim set; kindly address certain concessions evinced by certain cancellation(s) made in the prior 2 allowances.
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.
1. Claims 2-20 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 the genus, does not reasonably provide enablement for the species. 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 use the invention commensurate in scope with these claims.
It is being construed that the test sample is a portion of the sample, however, based upon the “test subject” divergence described below, the computer implemented invention is viewed as being directed to probabilities ostensibly obtainable from a single sampling.
By way of further explanation, computing meaningful probabilities from a single sampling for conditions that are, by their nature, estimated from populations (rather than a single-sample event), would require substantial, explicit disclosure of statistical methodology, assumptions, training/validation data, and error/uncertainty handling. The examiner found no such disclosure, thus, undue experimentation would be required.
Moreover, this field expects multi-sample aggregation or repeated measures to yield stable probabilities for the claimed conditions and there is no recognized approach to obtain a reliable probability from only a single measurement without population-trained parameters, the claims’ framing appears to be at odds with the art.
The written description requirement of 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph, applies to all claims including original claims that are part of the disclosure as filed. Ariad, 598 F.3d at 1349, 94 USPQ2d at 1170. As stated by the Federal Circuit, "[a]lthough many original claims will satisfy the written description requirement, certain claims may not." Id. at 1349, 94 USPQ2d at 1170-71; see also LizardTech, Inc. v. Earth Res. Mapping, Inc., 424 F.3d 1336, 1343-46, 76 USPQ2d 1724, 1730-33 (Fed. Cir. 2005); Regents of the Univ. of Cal. v. Eli Lilly & Co., 119 F.3d 1559, 1568, 43 USPQ2d 1398, 1405-06 (Fed. Cir. 1997)("The description requirement of the patent statute requires a description of an invention, not an indication of a result that one might achieve if one made that invention."). Problems satisfying the written description requirement for original claims often occur when claim language is generic or functional, or both. Ariad, 593 F.3d at 1349, 94 USPQ2d at 1171 ("The problem is especially acute with genus claims that use functional language to define the boundaries of a claimed genus. In such a case, the functional claim may simply claim a desired result, and may do so without describing species that achieve that result. But the specification must demonstrate that the applicant [inventor] has made a generic invention that achieves the claimed result and do so by showing that the applicant [inventor] has invented species sufficient to support a claim to the functionally-defined genus.").
For instance, generic claim language in the original disclosure does not satisfy the written description requirement if it fails to support the scope of the genus claimed. Ariad, 598 F.3d at 1349-50, 94 USPQ2d at 1171 ("[A]n adequate written description of a claimed genus requires more than a generic statement of an invention’s boundaries.") (citing Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1405-06); Enzo Biochem, Inc. v. Gen-Probe, Inc., 323 F.3d 956, 968, 63 USPQ2d 1609, 1616 (Fed. Cir. 2002) (holding that generic claim language appearing in ipsis verbis in the original specification did not satisfy the written description requirement because it failed to support the scope of the genus claimed); Fiers v. Revel, 984 F.2d 1164, 1170, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993) (rejecting the argument that "only similar language in the specification or original claims is necessary to satisfy the written description requirement").
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.
2. Claims 2-20 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.
Claim 2 recites a “a chromosome aneuploidy” in at least three instances---the preamble; step (c)(i)(1) and step (d). Claims 12 and 13 also both recite “a chromosome aneuploidy.” Clarification is respectfully requested.
Claim 9 recites “the test subject.” (emphasis added) There is insufficient antecedent basis for this particular subject which could be something like a person or a study. Moreover, there is not a (separate) determining step in claim 2 that fairly corresponds to the “determined” recitation in claim 9. Please consider adding step(s) to the independent claim wherein the necessary probabilities are provided and/or actually received and/or stored by the computer.
For the avoidance of doubt, claims 3-8, 10, 11 and 14-20 have defects through dependency.
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.
3. Claims 7, 8, 12 and 13 are 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.
As per claim 7, it is being construed that the recited condition does not exist in the sampling, such that the recited fraction etc. could not be computed in this particular instance.
As per claim 8, it is being construed that the recited (alternative) condition does not exist in the sampling, such that the recited fraction etc. could not be computed in this particular instance.
As per claim 12, it is being construed that there is an absence of the recited ploidy in the sampling, such that the recited determination could not be computed in this particular instance.
As per claim 13, it is being construed that there is the presence of the recited ploidy in the sampling, such that the recited determination could not be computed in this particular instance.
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.
It is noted that the not yet claimed combination / species suggested in claims 2/6/7/8 with the subject sample consisting of one or more mothers carrying fetuses, where both branches of the algorithm for having and not having certain (genetic) condition(s) are delineated together, possibly could be (re)written in independent form to overcome the above-described defects with respect to potentially operable statistical techniques for populations. (Similarly, the algorithm of 2/11/12/13 is noted.)
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
4. Claim 2 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,462,298.
Although the claims at issue are not identical, they are not patentably distinct from each other because they are both found to be directed to the same LOR algorithm for the same purpose. In the ‘298 patent, the claim is a computer-implemented method where certain steps expressly are performed with ‘a microprocessor’ which reasonably could be construed to be a different machine for each step which uses such tool(s). It would have been obvious to one skilled in the art to streamline the method to use a single device as reflected by the current preamble.
Current claim (Chromosome Aneuploidy Detection)
-Receives nucleic acid sequence reads from a test sample.
-Maps reads to portions of a reference genome.
-Determines counts mapped to portions.
-Creates a chromosome count representation.
-Calculates a log odds ratio (LOR) based on conditional and prior probabilities for aneuploidy vs. non-aneuploidy.
-Identifies presence or absence of chromosome aneuploidy.
Reference Claim (Microduplication/Microdeletion Detection)
-Receives nucleic acid sequence reads from a test sample obtained via non-targeted multiplexed massively parallel sequencing.
-Maps reads to portions of a reference genome.
-Normalizes counts of mapped reads.
-Segments normalized counts into discrete segments.
-Identifies a candidate segment.
-Calculates a log odds ratio (LOR) based on conditional and prior probabilities for microduplication/microdeletion vs. absence thereof.
-Determines presence or absence of microduplication/microdeletion.
The core analytical steps in both claims are substantially the same:
Obtaining nucleic acid sequence reads from circulating cell-free nucleic acids.
Mapping the reads to a reference genome.
Quantifying mapped reads.
Applying a statistical analysis (LOR) based on conditional and prior probabilities to detect a genomic abnormality.
The differences between the claims — namely, specifying massively parallel sequencing, normalization, segmentation, and targeting microduplication/microdeletion instead of chromosome aneuploidy — are considered obvious variations that a person of ordinary skill in the art would make when applying the same statistical methodology to different types of chromosomal abnormalities. The segmentation and normalization steps are routine data preprocessing methods in genomic analysis, and the substitution of microduplication/microdeletion for aneuploidy represents an obvious choice of target abnormality.
Accordingly, the present claim does not define a patentably distinct invention over the claims of the ‘298 patent , but rather constitute an obvious variation thereof.
Conclusion
Frudakis teaches a training phase that uses data from a sample population (counts individuals by genotype and trait), but once trained, the classifier operates on an individual without needing to re-estimate population parameters or polygenic risk scores; formalized a computer implemented pipeline: construct genotype-trait tables, perform correspondence analysis, then do discriminant analysis for classification.
Rabinowitz (earliest priority date: Aug. 17, 2012) discloses methods for determining the ploidy state of one or more chromosome in a developing fetus.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MICHAEL FUELLING whose telephone number is (571)270-1367.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/MICHAEL FUELLING/ Supervisory Patent Examiner