Prosecution Insights
Last updated: April 18, 2026
Application No. 17/597,760

SYSTEMS AND METHODS FOR CELL OF ORIGIN DETERMINATION FROM VARIANT CALLING DATA

Final Rejection §112
Filed
Jan 21, 2022
Examiner
SISSON, BRADLEY L
Art Unit
1682
Tech Center
1600 — Biotechnology & Organic Chemistry
Assignee
Roche Sequencing Solutions Inc.
OA Round
2 (Final)
20%
Grant Probability
At Risk
3-4
OA Rounds
5y 5m
To Grant
41%
With Interview

Examiner Intelligence

Grants only 20% of cases
20%
Career Allow Rate
145 granted / 743 resolved
-40.5% vs TC avg
Strong +21% interview lift
Without
With
+21.1%
Interview Lift
resolved cases with interview
Typical timeline
5y 5m
Avg Prosecution
77 currently pending
Career history
820
Total Applications
across all art units

Statute-Specific Performance

§101
20.1%
-19.9% vs TC avg
§103
20.2%
-19.8% vs TC avg
§102
7.4%
-32.6% vs TC avg
§112
45.8%
+5.8% vs TC avg
Black line = Tech Center average estimate • Based on career data from 743 resolved cases

Office Action

§112
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 . Drawings The drawings were received on 01 December 2025. These drawings are acceptable. Claim Interpretation Attention is directed to MPEP 904.01 [R-08.2012]. The breadth of the claims in the application should always be carefully noted; that is, the examiner should be fully aware of what the claims do not call for, as well as what they do require. During patent examination, the claims are given the broadest reasonable interpretation consistent with the specification. See In re Morris, 127 F.3d 1048, 44 USPQ2d 1023 (Fed. Cir. 1997). See MPEP § 2111 - § 2116.01 for case law pertinent to claim analysis. It is noted with particularity that narrowing limitations found in the specification cannot be inferred in the claims where the elements not set forth in the claims are linchpin of patentability. In re Philips Industries v. State Stove & Mfg. Co, Inc., 186 USPQ 458 (CA6 1975). While the claims are to be interpreted in light of the specification, it does not follow that limitations from the specification may be read into the claims. On the contrary, claims must be interpreted as broadly as their terms reasonably allow. See Ex parte Oetiker, 23 USPQ2d 1641 (BPAI, 1992). In added support of this position, attention is directed to MPEP 2111 [R-11.2013], where, citing In re Prater, 415 F.2d 1393, 1404-05, 162 USPQ 541, 550-51 (CCPA 1969), is stated: The court explained that “reading a claim in light of the specification, to thereby interpret limitations explicitly recited in the claim, is a quite different thing from ‘reading limitations of the specification into a claim,’ to thereby narrow the scope of the claim by implicitly adding disclosed limitations which have no express basis in the claim.” The court found that applicant was advocating the latter, i.e., the impermissible importation of subject matter from the specification into the claim. Additionally, attention is directed to MPEP 2111.01 [R-01.2024], wherein is stated: II. IT IS IMPROPER TO IMPORT CLAIM LIMITATIONS FROM THE SPECIFICATION “Though understanding the claim language may be aided by explanations contained in the written description, it is important not to import into a claim limitations that are not part of the claim. For example, a particular embodiment appearing in the written description may not be read into a claim when the claim language is broader than the embodiment.” Superguide Corp. v. DirecTV Enterprises, Inc., 358 F.3d 870, 875, 69 USPQ2d 1865, 1868 (Fed. Cir. 2004). Attention is also directed to MPEP 2111.02 II [R-07.2022]. As stated herein: II. PREAMBLE STATEMENTS RECITING PURPOSE OR INTENDED USE PNG media_image1.png 18 19 media_image1.png Greyscale The claim preamble must be read in the context of the entire claim. The determination of whether preamble recitations are structural limitations or mere statements of purpose or use "can be resolved only on review of the entirety of the [record] to gain an understanding of what the inventors actually invented and intended to encompass by the claim" as drafted without importing "'extraneous' limitations from the specification." Corning Glass Works, 868 F.2d at 1257, 9 USPQ2d at 1966. If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction. Shoes by Firebug LLC v. Stride Rite Children’s Grp., LLC, 962 F.3d 1362, 2020 USPQ2d 10701 (Fed. Cir. 2020) (The court found that the preamble in one patent’s claim is limiting but is not in a related patent); Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1305, 51 USPQ2d 1161, 1165 (Fed. Cir. 1999). See also Rowe v. Dror, 112 F.3d 473, 478, 42 USPQ2d 1550, 1553 (Fed. Cir. 1997) ("where a patentee defines a structurally complete invention in the claim body and uses the preamble only to state a purpose or intended use for the invention, the preamble is not a claim limitation")… (Emphasis added) Attention is directed to MPEP 2111 [R-10.2019]. As stated therein: During patent examination, the pending claims must be "given their broadest reasonable interpretation consistent with the specification." The Federal Circuit’s en banc decision in Phillips v. AWH Corp., 415 F.3d 1303, 1316, 75 USPQ2d 1321, 1329 (Fed. Cir. 2005) expressly recognized that the USPTO employs the "broadest reasonable interpretation" standard: The Patent and Trademark Office ("PTO") determines the scope of claims in patent applications not solely on the basis of the claim language, but upon giving claims their broadest reasonable construction "in light of the specification as it would be interpreted by one of ordinary skill in the art." In re Am. Acad. of Sci. Tech. Ctr., 367 F.3d 1359, 1364[, 70 USPQ2d 1827, 1830] (Fed. Cir. 2004). Indeed, the rules of the PTO require that application claims must "conform to the invention as set forth in the remainder of the specification and the terms and phrases used in the claims must find clear support or antecedent basis in the description so that the meaning of the terms in the claims may be ascertainable by reference to the description." 37 CFR 1.75(d)(1). (Emphasis added). Attention is directed to MPEP 2173.04 [R-10.2019]. As stated therein: Breadth of a claim is not to be equated with indefiniteness. In re Miller, 441 F.2d 689, 169 USPQ 597 (CCPA 1971); In re Gardner, 427 F.2d 786, 788, 166 USPQ 138, 140 (CCPA 1970) ("Breadth is not indefiniteness."). A broad claim is not indefinite merely because it encompasses a wide scope of subject matter provided the scope is clearly defined. But a claim is indefinite when the boundaries of the protected subject matter are not clearly delineated and the scope is unclear. For example, a genus claim that covers multiple species is broad, but is not indefinite because of its breadth, which is otherwise clear. But a genus claim that could be interpreted in such a way that it is not clear which species are covered would be indefinite (e.g., because there is more than one reasonable interpretation of what species are included in the claim). (Emphasis added) Claim Rejections - 35 USC § 112, Second Paragraph / (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. Standard for Definiteness. Attention is directed to MPEP 2171 [R-11.2013]: Two separate requirements are set forth in 35 U.S.C. 112(b) and pre-AIA 35 U.S.C. 112, second paragraph, namely that: (A) the claims must set forth the subject matter that the inventor or a joint inventor regards as the invention; and (B) the claims must particularly point out and distinctly define the metes and bounds of the subject matter to be protected by the patent grant. The first requirement is a subjective one because it is dependent on what the inventor or a joint inventor for a patent regards as his or her invention. Note that although pre-AIA 35 U.S.C. 112, second paragraph, uses the phrase "which applicant regards as his invention," pre-AIA 37 CFR 1.41(a) provides that a patent is applied for in the name or names of the actual inventor or inventors. The second requirement is an objective one because it is not dependent on the views of the inventor or any particular individual, but is evaluated in the context of whether the claim is definite — i.e., whether the scope of the claim is clear to a hypothetical person possessing the ordinary level of skill in the pertinent art. Attention is directed to MPEP 2173.02 I [R-01.2024]: During prosecution, applicant has an opportunity and a duty to amend ambiguous claims to clearly and precisely define the metes and bounds of the claimed invention. The claim places the public on notice of the scope of the patentee’s right to exclude. See, e.g., Johnson & Johnston Assoc. Inc. v. R.E. Serv. Co., 285 F.3d 1046, 1052, 62 USPQ2d 1225, 1228 (Fed. Cir. 2002) (en banc). As the Federal Circuit stated in Halliburton Energy Servs., Inc. v. M-I LLC, 514 F.3d 1244, 1255, 85 USPQ2d 1654, 1663 (Fed. Cir. 2008): “We note that the patent drafter is in the best position to resolve the ambiguity in the patent claims, and it is highly desirable that patent examiners demand that applicants do so in appropriate circumstances so that the patent can be amended during prosecution rather than attempting to resolve the ambiguity in litigation.” *** During examination, after applying the broadest reasonable interpretation to the claim, if the metes and bounds of the claimed invention are not clear, the claim is indefinite and should be rejected. Packard, 751 F.3d at 1310 (“[W]hen the USPTO has initially issued a well-grounded rejection that identifies ways in which language in a claim is ambiguous, vague, incoherent, opaque, or otherwise unclear in describing and defining the claimed invention, and thereafter the applicant fails to provide a satisfactory response, the USPTO can properly reject the claim as failing to meet the statutory requirements of § 112(b).”); Zletz, 893 F.2d at 322, 13 USPQ2d at 1322. Attention is also directed to MPEP 2173.02 III B [R-01-2024], which states in part: To comply with 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph, applicants are required to make the terms that are used to define the invention clear and precise, so that the metes and bounds of the subject matter that will be protected by the patent grant can be ascertained. See MPEP § 2173.05(a), subsection I. It is important that a person of ordinary skill in the art be able to interpret the metes and bounds of the claims so as to understand how to avoid infringement of the patent that ultimately issues from the application being examined. See MPEP § 2173.02, subsection II (citing Morton Int ’l, Inc. v. Cardinal Chem. Co., 5 F.3d 1464, 1470 (Fed. Cir. 1993)); see also Halliburton Energy Servs., 514 F.3d at 1249, 85 USPQ2d at 1658 (“Otherwise, competitors cannot avoid infringement, defeating the public notice function of patent claims.”). Examiners should bear in mind that “[a]n essential purpose of patent examination is to fashion claims that are precise, clear, correct, and unambiguous. Only in this way can uncertainties of claim scope be removed, as much as possible, during the administrative process.” Zletz, 893 F.2d at 322, 13 USPQ2d at 1322 [Fed. Cir. 1989]. (Emphasis added) Attention is also directed to MPEP 2173.04 [R-10-2019], which states in part: A broad claim is not indefinite merely because it encompasses a wide scope of subject matter provided the scope is clearly defined. But a claim is indefinite when the boundaries of the protected subject matter are not clearly delineated and the scope is unclear. For example, a genus claim that covers multiple species is broad, but is not indefinite because of its breadth, which is otherwise clear. But a genus claim that could be interpreted in such a way that it is not clear which species are covered would be indefinite (e.g., because there is more than one reasonable interpretation of what species are included in the claim). Holding and Rationale Claims 1-15 and 18-23 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. Claims 1 and 12 are indefinite with respect to just which genes were identified. Acknowledgement is made of dependent claims 3-6 specifying the genes of claim 1, and that dependent claims 19 and 20 specify the genes for independent claim 12. Given that a dependent claim must further limit the claim from which it depends, it is unclear as to just which other gene(s) is/are encompassed in each of the methods of claims 1 and 12. Claims 2-11, which depend from claim 1, and claims 13-15 and 18-23, which depend from claim 12, fail to overcome the above identified issue and are similarly rejected. Claim Rejections - 35 USC § 112, Written Description 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. Standard for Written Description. Attention is directed to MPEP 2163.02 Standard for Determining Compliance With the Written Description Requirement [R-07-2022]: An objective standard for determining compliance with the written description requirement is, "does the description clearly allow persons of ordinary skill in the art to recognize that he or she invented what is claimed." In re Gosteli, 872 F.2d 1008, 1012, 10 USPQ2d 1614, 1618 (Fed. Cir. 1989). Under Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Fed. Cir. 1991), to satisfy the written description requirement, an applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention, and that the invention, in that context, is whatever is now claimed. (Emphasis added) Attention is also set directed to MPEP 2161.01 I [R-07-2022], wherein is stated: 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"). As set forth in Fiers v. Revel 25 USPQ2d 1601, 1604-5 (CAFC, January 1993): We thus determined that, irrespective of the complexity or simplicity of the method of isolation employed, conception of a DNA, like conception of any chemical substance, requires a definition of that substance other than by its functional utility. Fiers' attempt to distinguish Amgen therefore is incorrect. We also reject Fiers' argument that the existence of a workable method for preparing a DNA establishes conception of that material. (Emphasis added) Conception of a substance claimed per se without reference to a process requires conception of its structure, name, formula, or definitive chemical or physical properties... The difficulty that would arise if we were to hold that a conception occurs when one has only an idea of a compound, defining it by its hoped-for function, is that would-be inventors would file patent applications before they had made their inventions and before they could describe them. That is not consistent with the statute or the policy behind the statute, which is to promote disclosure of inventions. As set forth in the en banc decision in Ariad Pharmaceuticals Inc. v. Eli Lilly and Company, 94 USPQ2d 1161 (Fed. Cir. 2010) at 1171: We held that a sufficient description of a genus instead requires the disclosure of either a representative number of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can “visualize or recognize” the members of the genus. Id. at 1568-69. We explained that an adequate written description requires a precise definition, such as by structure, formula, chemical name, physical properties, or other properties, of species falling within the genus sufficient to distinguish the genus from other materials. Id. at 1568 (quoting Fiers v. Revel, 984 F.2d 1164, 1171 [25 USPQ2d 1601] (Fed. Cir. 1993)). We have also held that functional claim language can meet the written description requirement when the art has established a correlation between structure and function. See Enzo, 323 F.3d at 964 (quoting 66 Fed. Reg. 1099 (Jan. 5, 2001)). But merely drawing a fence around the outer limits of a purported genus is not an adequate substitute for describing a variety of materials constituting the genus and showing that one has invented a genus and not just a species. *** In Fiers, we rejected the argument that “only similar language in the specification or original claim is necessary to satisfy the written description requirement.” 984 F.2d at 1170 (emphasis added). Rather, we held that original claim language to “a DNA coding for interferon activity” failed to provide an adequate written description as it amounted to no more than a “wish” or “plan” for obtaining the claimed DNA rather than a description of the DNA itself. Id. at 1170-71. That Fiers applied § 112, first paragraph, during an interference is irrelevant for, as we stated above, the statute contains no basis for ignoring the description requirement outside of this context. And again in Enzo we held that generic claim language appearing in ipsis verbis in the original specification does not satisfy the written description requirement if it fails to support the scope of the genus claimed. 323 F.3d at 968. We concluded that “[a] claim does not become more descriptive by its repetition, or its longevity.” Id. at 969. *** The written description requirement also ensures that when a patent claims a genus by its function or result, the specification recites sufficient materials to accomplish that function—a problem that is particularly acute in the biological arts. Attention is also directed to MPEP 2163 Guidelines for the Examination of Patent Applications Under the 35 U.S.C. 112(a) or Pre-AIA 35 U.S.C. 112, first paragraph, “Written Description” Requirement [R-01-2024], at part II ii): The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice (see i)(A) above), reduction to drawings (see i)(B) above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the inventor was in possession of the claimed genus (see i)(C) above). See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. See Juno Therapeutics, Inc. v. Kite Pharma, Inc., 10 F.4th 1330, 1337, 2021 USPQ2d 893 (Fed. Cir. 2021) ( "[T]he written description must lead a person of ordinary skill in the art to understand that the inventor possessed the entire scope of the claimed invention. Ariad, 598 F.3d at 1353–54 ('[T]he purpose of the written description requirement is to ensure that the scope of the right to exclude, as set forth in the claims, does not overreach the scope of the inventor's contribution to the field of art as described in the patent specification.' (internal quotation marks omitted).") (Emphasis added) Acknowledgement is made of the fact that the claims are to a method and not to a product. However, it is well settled that in order to satisfy the written description for a method, one must also disclose the molecules required to perform the method. In support of this position attention is directed to University of Rochester v. G.D. Searle & Co. 68 USPQ2D 1424 (W.D.N.Y. 2003) at 1433 (affirmed; University of Rochester v. G.D. Searle & Co. 69 USPQ2d 1886 (Fed. Cir. 2004)): Plaintiff also argues that the requirements for written descriptions of claims to chemical compounds are irrelevant to this case because the '850 patent does not claim a compound, but a method of treatment by targeting PGHS-2 activity over PGHS-1 activity. Virtually any compound claim could be transformed into a method claim, however, simply by means of wording the claim in terms of a method of using the compound. With respect to the issue before the Court, then, this is little more than a semantic distinction without a difference. The claimed method depends upon finding a compound that selectively inhibits PGHS-2 activity. Without such a compound, it is impossible to practice the claimed method of treatment. It means little to “invent” a method if one does not have possession of a substance that is essential to practicing that method. Without that substance, the claimed invention is more theoretical than real; it is, as defendants argue, akin to “inventing” a cure for cancer by utilizing a substance that attacks and destroys cancer cells while leaving healthy cells alone. Without possession of such a substance, such a “cure” is illusory, and there is no meaningful possession of the method. *** What the inventors did not do, however, is succeed in taking the last, critical step of actually isolating such a compound, or at least of developing a process through which one skilled in the art would be directly led to such a compound. Absent that step, their discoveries, valuable though they might have been, did not blossom into a full-fledged, complete invention. Scientific discoveries, and theories based on those discoveries, frequently lay the groundwork for later inventions, but that does not make the discoverer the inventor as well. Attention is also directed to the decision in Ariad Pharmaceuticals Inc. v. Eli Lilly & Co. (Fed. Cir. 2010) 94 USPQ2d 1161, 1175, which teaches: In accordance with Rochester, the ?516 patent must adequately describe the claimed methods for reducing NF-?B activity, including adequate description of the molecules that Ariad admits are necessary to perform the methods. (Emphasis added) Holding and Rationale Claims 1-15 and 18-23 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. Claims 1 and 12 are the only independent claims pending. Claims 1, 6, 7, 12, 20, and 21 are deemed to be representative and, for convenience, are reproduced below. PNG media_image2.png 285 571 media_image2.png Greyscale PNG media_image3.png 388 572 media_image3.png Greyscale PNG media_image4.png 57 564 media_image4.png Greyscale PNG media_image5.png 300 574 media_image5.png Greyscale PNG media_image6.png 152 566 media_image6.png Greyscale PNG media_image7.png 160 583 media_image7.png Greyscale PNG media_image8.png 48 566 media_image8.png Greyscale The claims are drawn to “a computer-implemented method for classifying a cell of origin for a type of lymphoma” in a human subject. As presently worded, the claimed method encompasses the use of virtually any “plurality of decision trees based on a collection of features”. In support of this position attention is directed to paragraph [00057], wherein applicant asserts: [00057] Different machine learning algorithms may be useful for COO classification. For example, ensemble based machine learning algorithms and/or decision tree based machine learning algorithms can be used to perform COO classification. Ensemble methods combine multiple learning algorithm algorithms into a single aggregate model. For example, a model based on a plurality of decision trees can be considered an ensemble method. Decision tree algorithms include (1) a basic decision tree based on a plurality of conditions; (2) a bootstrap aggregating or bagging algorithm is an ensemble algorithm that combines predictions from a plurality of decision trees through a majority voting approach; (3) a random forest algorithm is a bagging-based algorithm where only a subset of features are selected at random for each decision tree to build a plurality (i.e., a forest) of decision trees; (4) a boosting algorithm builds each decision tree sequentially by minimizing the errors from previous models (i.e., decision trees) while increasing (i.e. boosting) the weight or influence of high-performing models (i.e. decision trees); ( 5) a gradient boosting algorithm uses a gradient descent algorithm to minimize errors in sequential model (i.e. boosting algorithm in (4)); and (6) optimized gradient boosting algorithm in (i.e. XGBoost) which may employ parallel processing, tree-pruning, handling missing values, and regularization to reduce overfitting and/or bias in gradient boosting algorithms. Any of these algorithms, alone or in combination, can be used for the COO classifier. (Emphasis added) The capacity of the processor is without limit, as is the computer language, and as is the format of any data to be analyzed by any of the aforementioned algorithm(s). A review of the disclosure fails to find any example, much less the nucleotide sequence of any genes found in any organism listed in the Markush groups found in each of claims 3-6, 19, and 20. The nucleotide sequences of these genes is deemed to constitute essential material.1 As evidenced above, the claims are directed to “a computer-implemented method”. A review of the disclosure fails to find where applicant has provided the algorithms for the genus of “decision trees” that the claimed “computer-implemented method” must use. A review of the disclosure does identify any schematic of how the computer system may be configured. However, a flow diagram of the computer program has not been located. Likewise, a review of the disclosure fails to find a computer program in any language. In view of the above analysis and in the absence of convincing evidence to the contrary, claims 1-15, and 18-23 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. Response to traversal Applicant’s representative, at pages 17-20 of the response of 28 April 2025, hereinafter the response, traverses the rejection of claims under 35 USC 112 for not satisfying the written description requirement. At page 18 of the response said representative asserts: One of ordinary skill in the art, using the specific gene identifiers disclosed in the Specification, could/can readily access and obtain the respective sequences from a variety of public sources (see, e.g., https://www.ncbi.nlm.nih.gov/). Simply, there is no basis for the Examiner's assertion that reproducing the complete sequence listings in the Specification was necessary for one of ordinary skill in the art to make and use the claimed invention. The above argument has been considered and has not been found persuasive towards the removal of the rejection. In support of this position attention is directed to 37 CFR 1.57(d) and (e). (See footnote on page 14.) As can be seen, essential material, material that is necessary to satisfy the written description requirement may be incorporated by reference to either a US patent or a US patent application publication. As can be seen in 37 CFR 1.57(e), “incorporation by reference by hyperlink or other form of browser executable code is not permitted”. (Emphasis added) Given such, the aspect that the sequences necessary to satisfy the enablement and written description requirements are available via a hyperlink does not satisfy the written description requirement. Therefore, and in the absence of convincing evidence to the contrary, the rejection is maintained. At pages 19-20 of the response attention is directed to various figures as providing flow diagrams relevant to the claimed method. For convenience, FIG. 4 is reproduced below. PNG media_image9.png 540 627 media_image9.png Greyscale While the flow diagram identifies major areas for analysis, the diagram does not identify which decisions in the various decision trees are to be generated. For example, the figure is silent as to what steps are to be performed when one wants to “Calculate Errors”, much less “Train Model Predicting Errors”. In view of the above analysis and in the absence of convincing evidence to the contrary, the rejection is maintained. Conclusion Objections and/or rejections which appeared in the prior Office action and which have not been repeated hereinabove have been withdrawn. The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. US 2017/0029904 A1 (Rodig et al.) US 2017/0175199 A1 (Magliocco et al.) Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a). A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action. Any inquiry concerning this communication or earlier communications from the examiner should be directed to Bradley L. Sisson whose telephone number is (571)272-0751. The examiner can normally be reached Monday to Thursday, from 6:30 AM to 5 PM.. Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Shen can be reached at 571-272-3157. 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. /Bradley L. Sisson/Primary Examiner, Art Unit 1682 1 Attention is directed to 37 CFR 1.57(d) and (e), which sates in part: (d) "Essential material" may be incorporated by reference, but only by way of an incorporation by reference to a U.S. patent or U.S. patent application publication, which patent or patent application publication does not itself incorporate such essential material by reference. "Essential material" is material that is necessary to: (1) Provide a written description of the claimed 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 set forth the best mode contemplated by the inventor of carrying out the invention as required by 35 U.S.C. 112(a); (2) Describe the claimed invention in terms that particularly point out and distinctly claim the invention as required by 35 U.S.C. 112(b); or (3) Describe the structure, material, or acts that correspond to a claimed means or step for performing a specified function as required by 35 U.S.C. 112(f). (Emphasis added) (e) Other material ("Nonessential material") may be incorporated by reference to U.S. patents, U.S. patent application publications, foreign patents, foreign published applications, prior and concurrently filed commonly owned U.S. applications, or non-patent publications. An incorporation by reference by hyperlink or other form of browser executable code is not permitted. (Emphasis added)
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Prosecution Timeline

Jan 21, 2022
Application Filed
Feb 26, 2025
Non-Final Rejection — §112
Apr 01, 2025
Interview Requested
Apr 09, 2025
Examiner Interview Summary
Apr 09, 2025
Applicant Interview (Telephonic)
Apr 24, 2025
Response Filed
Apr 24, 2025
Response after Non-Final Action
May 22, 2025
Response Filed
May 22, 2025
Response after Non-Final Action
Dec 01, 2025
Response Filed
Apr 07, 2026
Final Rejection — §112 (current)

Precedent Cases

Applications granted by this same examiner with similar technology

Patent 12529100
METHODS FOR REMOVAL OF ADAPTOR DIMERS FROM NUCLEIC ACID SEQUENCING PREPARATIONS
2y 5m to grant Granted Jan 20, 2026
Patent 12492424
COMPOSITIONS AND METHODS FOR DETECTING VIRAL NUCLEIC ACIDS
2y 5m to grant Granted Dec 09, 2025
Patent 12410463
NOVEL MOLECULAR BEACONS
2y 5m to grant Granted Sep 09, 2025
Patent 12404543
HYBRIDIZATION COMPOSITIONS AND METHODS FOR MAKING AND USING COMPOSITIONS
2y 5m to grant Granted Sep 02, 2025
Patent 12385089
METHODS FOR SINGLE-MOLECULE ANALYSIS
2y 5m to grant Granted Aug 12, 2025
Study what changed to get past this examiner. Based on 5 most recent grants.

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Prosecution Projections

3-4
Expected OA Rounds
20%
Grant Probability
41%
With Interview (+21.1%)
5y 5m
Median Time to Grant
Moderate
PTA Risk
Based on 743 resolved cases by this examiner. Grant probability derived from career allow rate.

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