DETAILED CORRESPONDENCE
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 .
This action is in response to the papers filed July 16, 2026. Currently, claims 1-30 are pending. Claims 6-8 have been withdrawn as drawn to non-elected subject matter.
Election/Restrictions
Applicant's election without traverse of PLGRKT, lung cancer and Pd-1 inhibitor in the paper filed July 16, 2026 is acknowledged.
The requirement is still deemed proper and is therefore made FINAL.
Priority
This application claims priority to
Drawings
The drawings are acceptable.
Information Disclosure Statement
It is noted that the IDS filed May 13, 2024, contains an extremely large number of reference for consideration by the Examiner. If the Applicant and/or Applicant and/or Applicant's representative are aware of any particular reference or portion of a reference in the extensive list which the examiner should pay particular attention to, it is required that it be specifically pointed out in response to this Office action.
Applicant is reminded that "burying" relevant references in a lengthy IDS is discouraged. See, e.g., Molins PLC v. Textron Inc., 48 F.3d 1172, 33 USPQ2d 1823, 1831 (Fed. Cir. 1995) The court concluded that, by “burying” Wagenseil in a multitude of other references, Hirsh and Smith intentionally withheld it from the PTO because this manner of disclosure was tantamount to a failure to disclose. Citing Penn Yan Boats, Inc. v. Sea Lark Boats, Inc., 359 F.Supp. 948, 175 USPQ 260 (S.D. Fla. 1972), aff'd, 479 F.2d 1328, 178 USPQ 577 (5th Cir.), cert. denied, 414 U.S. 874 (1973), the court stated that Hirsh's and Smith's failure to highlight Wagenseil in light of their knowledge of Whitson's actions in the foreign prosecutions violated their duty of candor to the PTO. Citing our precedent, Tetron asserts that Smith's and Hirsh's conduct is “inexcusable, fraudulent, and cannot operate to cure Whitson's inequitable conduct.” See Rohm & Haas Co. v. Crystal Chem. Co., 722 F.2d 1556, 220 USPQ 289 (Fed.Cir. 1983), cert. denied, 469 U.S. 851 (1984) (where intentional material misrepresentations have been made, a “cure” through voluntary efforts during prosecution must be demonstrated by clear, unequivocal, and convincing evidence).
Improper Markush Rejection
Claims 1-5, 9-16, 18-30 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984).
A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
A Markush claim contains an “improper Markush grouping” if:
(1) the species of the Markush group do not share a “single structural similarity,” or (2) the species do not share a common use. Members of a Markush group share a “single structural similarity” when they belong to the same recognized physical or chemical class or to the same art-recognized class. Members of a Markush group share a common use when they are disclosed in the specification or known in the art to be functionally equivalent. See MPEP § 2117.
Here each species is considered to be each of the fusion partners and chromosomal coordinates. The recited alternative species in the groups set forth here do not share a single structural similarity, as each different fusion partner or chromosomal position is itself located in a separate region of the genome and has its own structure. The fusion partners and chromosomal positions recited in the instant claims, do not share a single structural similarity since each consists of a different nucleotide sequences with functions. As illustrated in Table 3, some of the fusions are associated with bladder carcinoma, others with skin melanoma, others with SCC, for example. The specification has not identified any common use that flows from a substantial structural feature.
The only structural similarity present is that all detected positions are part of nucleic acid molecules. The fact that the markers comprise nucleotides per se does not support a conclusion that they have a common single structural similarity because the structure of comprising a nucleotide alone is not essential to a common activity.
MPEP 2117 (II)(A) provides the following guidance as to what constitutes a physical, chemical, or art recognized class:
A recognized physical class, a recognized chemical class, or an art-recognized class is a class wherein “there is an expectation from the knowledge in the art that members of the class will behave in the same way in the context of the claimed invention. In other words, each member could be substituted one for the other, with the expectation that the same intended result would be achieved”
The recited fusion partners and chromosomal coordinates do not belong to a recognized chemical class because there is no expectation from the knowledge in the art that the fusion partners and chromosomal coordinates will behave in the same manner and can be substituted for one another with the same intended result achieved. In other words, there is no expectation from the knowledge in the art that each of the recited fusion partners and chromosomal coordinates would function in the same way in the claimed method; it is only in the context of this specification that it was disclosed that all members of this group may behave in the same way in the context of the claimed invention. Further there is no evidence of record to establish that it is clear from their very nature that each of the recited genes possess a common property.
MPEP 2117 (II) further states the following:
Where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the compounds do not appear to be members of a recognized physical or chemical class or members of an art-recognized class, the members are considered to share a "single structural similarity" and common use when the alternatively usable compounds share a substantial structural feature that is essential to a common use. Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984).
The recited alternative species do not share a substantial common structure just because they all have a sugar phosphate backbone. The sugar phosphate backbone of a nucleic acid chain is not considered to be a substantial common structural feature to the group of genes being claimed because it is shared by ALL nucleic acids. A feature that is ubiquitous in the art can not be a substantial structural feature that is essential to a common use. The fact that the genes all have a sugar phosphate backbone does not support a conclusion that they have a common single structural similarity because the structure of comprising a sugar phosphate backbone alone is not essential to a common use.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1, 9-16, 18-30 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
35 U.S.C. § 101 requires that to be patent-eligible, an invention (1) must be directed to one of the four statutory categories, and (2) must not be wholly directed to subject matter encompassing a judicially recognized exception. M.P.E.P. § 2106. Regarding judicial exceptions, “[p]henomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.” Gottschalk v. Benson, 409 U.S. 63, 67 (1972); see also M.P.E.P. § 2106, part II.
Based upon consideration of the claims as a whole, as well as consideration of elements/steps recited in addition to the judicial exception, the present claims fail to meet the elements required for patent eligibility.
Question 1
The claimed invention is directed to a process that involves a natural principle and a judicial exception.
Question 2A Prong I
The claims are taken to be directed to an abstract idea, a law of nature and a natural phenomenon.
Claim 1 is directed to “a method of selecting a treatment for an individual having a cancer” comprising acquiring knowledge of a CD274 molecule. The claim provides a wherein clause that recites the knowledge identifies the individual as one who may benefit from at treatment comprising an immune checkpoint inhibitor.
Claim 1 is directed to a process that involves the judicial exceptions of an abstract idea (i.e. the abstract steps of “acquiring knowledge”) and a law of nature/natural phenomenon (i.e. the natural correlation between the presence of a CD274 fusion identifies the individual as one who may benefit from a treatment comprising an immune checkpoint inhibitor).
Claim 5 is similarly directed to selecting a treatment based on the generated genomic profile. This is a correlation between genomic profile and treatment selection.
Claims 20 are directed to predicting that a sample from a tumor is PD-L1 high positive based on the number of read pairs.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception for the reasons that follow.
Herein, claim 1 involves the patent-ineligible concept of an abstract process. Claim 1 requires performing the step of “detecting or acquiring knowledge”. Neither the specification nor the claims set forth a limiting definition for "detecting” or “acquiring knowledge", “selecting a treatment” and the claims do not set forth how either of these steps may be accomplished. As broadly recited, both selecting, detecting and acquiring knowledge may be accomplished mentally by thinking about a subject’s CD274 nucleic acid. Thus, the detecting and acquiring knowledge step constitutes an abstract process idea.
A correlation that preexists in the human is an unpatentable phenomenon. The association between CD274 nucleic acid molecules and association with benefit from a treatment with an immune checkpoint inhibitor is a law of nature/natural phenomenon. The wherein clause tells users of the process to predict individual as one who may benefit from a treatment comprising an immune checkpoint inhibitor, amounts to no more than an "instruction to apply the natural law". This wherein clause is no more than a mental step. Even if the wherein clause requires something more such as to verbalize the discovery of the natural law, this mere verbalization is not an application of the law of nature to a new and useful end. The wherein clause does not require the process user to do anything in light of the correlation. The wherein clause fails to provide the “practical assurance” sought by the Prometheus Court that the “process is more than a drafting effort designed to monopolize the law of nature itself.”
Claims 20-21 are similarly directed to wherein clauses for predicating a tumor is PD-L1 high positive based on sequencing reads.
Claim 22 recites additional inherent properties and natural phenomena.
Question 2A Prong II
The exception is not integrated into a practical application of the exception. The claims do not recite any additional elements that integrate the exception into a practical application of the exception. While the claim recites selecting a treatment for an individual, this is not an integration of the exception into a practical application. Selection of a treatment does not require administering the treatment. The plain and ordinary meaning of selecting a treatment does not require that the selecting occur in writing and encompasses orally telling an individual in need thereof to take a particular course of action. The plain and ordinary meaning of “selecting” also does not require that the individual in need thereof do anything other than receive, such as, hear, a recommendation. Selecting a treatment does not integrate the natural phenomenon because it is merely an instruction regarding therapy but does not require the therapy to be delivered or administered. Thus, the claim is “directed to” the exception.
Question 2B
The second step of Alice involves determining whether the remaining elements, either in isolation or combination with the other non patent ineligible elements, are sufficient to “’transform the nature of the claim’ into a patent eligible application” Alice, 134 S. Ct. at 2355 (quoting Mayo, 132 S. Ct. at 1297).
The claims are not sufficiently defined to provide a method which is significantly more from a statement of a natural principle for at least these reasons:
The claims do not include applying the judicial exception, or by use of, a particular machine. The claims do not tie the steps to a “particular machine" and therefore do not meet the machine or transformation test on these grounds. The use of machines generally does not impose a meaningful limit on claim scope.
The claims also do not add a specific limitation other than what is well-understood, routine and conventional in the field. If detecting a CD274 nucleic acid molecule is read to require a particular protocol, the steps are mere data gathering step that amounts to extra solution activity to the judicial exception. It merely tells the users of the method to detecting a CD274 nucleic acid without further specification as to how the sample should be analyzed. The claim does not recite a new, innovative method for such determination. The determining step essentially tells users to determine the markers through whatever known processes they wish to use.
The step of determining CD274 rearrangements was well known in the art at the time the invention was made. The steps are recited at a high level of generality. The claim merely instructs a scientist to use any assay determine the presence of the rearrangement. The claim does not require the use of any particular non-conventional reagents. When recited at this high level of generality, there is no meaningful limitation that distinguishes this step from well understood, routine and conventional activities engaged in by scientists prior to applicant’s invention and at the time the application was filed.
Further it is noted that the courts have recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity.
Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546;
Amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014)
For these reasons the claims are rejected under section 101 as being directed to non-statutory subject matter.
Claim Rejections - 35 USC § 112- Second Paragraph
The following is a quotation of 35 U.S.C. 112(b):
(B) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1-5, 9-30 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 pre-AIA the applicant regards as the invention.
A) The claim refers to tables. MPEP 2173.05(s) states:
Where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table “is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience.” Ex parte Fressola, 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993) (citations omitted).
The claims recite Table 1-3. Appropriate correction is required.
B) Claims 1-2, 9-30 are indefinite. It is not clear how the recited preamble is intended to breathe life and meaning into the claim. The preamble of Claim 1 is directed to a method for selecting a treatment for an individual. However, the claim only provides for detecting or acquiring knowledge of a CD274 nucleic acid molecule. Thus, it is not clear if applicants intend to cover any method for detecting or acquiring knowledge of a CD274 nucleic acid molecule, or if the method is intended to somehow require more to accomplish the goal set forth in the preamble. If the claim requires something more, it is unclear what additional active process step the method requires and it appears that the claims are incomplete. The claims fail to provide any active steps that clearly accomplish the goal set forth by the preamble of the claims. Claims 9-30 are similarly indefinite
C) Claim 2 is indefinite because it is unclear how the recited preamble is intended to breathe life and meaning into the claim. The preamble of Claim 2 is directed to a method for treating or delaying progress of cancer. However, the claim only provides for detecting or acquiring knowledge of a CD274 nucleic acid molecule and administering to the individual an effective amount of a treatment. The claim does not provide whether the mere treatment is a method for delaying progression or whether something more is required. Thus, it is not clear if applicants intend to cover any method for detecting or acquiring knowledge of a CD274 nucleic acid molecule with a treatment, or if the method is intended to somehow require more to accomplish the goal set forth in the preamble. If the claim requires something more, it is unclear what additional active process step the method requires and it appears that the claims are incomplete. The claims fail to provide any active steps that clearly accomplish the goal set forth by the preamble of the claims.
Even more, it is unclear whether all individuals are treated or only individuals with a breakpoint/fusion are treated. The metes and bounds of the invention are unclear.
D) Claim 3 is indefinite over the recitation the “chromosomal coordinates as listed in Table 1” because the chromosomal coordinates do not have any context. It is unclear what the numbering system is and how to detect the positions recited. There is not reference sequence or clarity for which genome collection is being referred to. Correction is required.
Claim Rejections - 35 USC § 102
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.
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 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.
Claim(s) 1-2, 10-16, 18-25, 30 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by The Cancer Genome Atlas Network (Nature, Vol. 517, pages 576-582, 2015) as evidenced by FusionGDB2 (PLGRKT-CD274 (FusionGDB2 ID: 65934, 2021).
With respect to Claim 1, The Cancer Genome Atlas Network teaches characterization of neck squamous cell carcinomas using Next generation sequencing.
FusionGDB2 (PLGRKT-CD274 (FusionGDB2 ID: 65934) teaches the rearrangement was identified in TCGA-CV-5443-01A sample. This was a sample from a 63 year old male for the TCGA program. Thus, TCGA-CV-5443-01A teaches all of the limitations of detecting knowledge of CD274.
With respect to Claim 2, the PLGRKT-CD274 (FusionGDB2 ID: 65934) was not found in 278 patients in The cancer Genome Atlas. Thus, no treatment is required by the claims.
With respect to Claim 10-13, the claim does not require a method step of administering the treatment, so the limitations of the agents do not limit the instant claims.
With respect to Claim 14-16, the analysis of The Cancer Genome Atlas Network analyzes samples for mutations and detects the presence or absence. The claims do not require any particular result is detected.
With respect to Claim 18-21, analysis of clonality is not required but one of several alternatives, thus, clonality analysis is not particularly required.
With respect to Claim 22, the claim recites inherent properties and does not further require any additional method steps.
With respect to Claims 23-24, tumors were analyzed (page 576, col. 1).
With respect to Claim 25, the analysis was performed using RNA-Seq (page 576, col. 1).
With respect to Claim 30, the individual was a human.
Claim(s) 1-5, 9-16, 18-30 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Huang et al. (WO2022/241293, provisional May 14, 2021).
Claim(s) 1-5, 9-16, 18-30 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Huang et al. (US 2024/0263240, provisional May 14, 2021).
The applied reference has a common assignee and inventor with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2). This rejection under 35 U.S.C. 102(a)(2) might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C. 102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B) if the same invention is not being claimed; or (3) a statement pursuant to 35 U.S.C.102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed in the copending application and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement.
With respect to Claims 1, 14, Huang teaches CD274 mutations of cancer treatment. Huang teaches detecting or acquiring knowledge of CD274/PLGRKT fusion (para 159 and Table 9). Claim 1 does not require any additional active method steps. Even if the claim is amended to add an additional step of selecting a treatment, Huang teaches acquiring knowledge of CD274 and selecting a treatment (para 133).
With respect to Claim 2, Huang teaches acquiring knowledge of CD274 and selecting a treatment (para 133 and 360).
With respect to Claim 3-5, Huang teaches detecting CD274 using NGS methods. The method comprising: (a) providing a plurality of nucleic acids obtained from a sample from an individual, wherein the plurality of nucleic acids comprises nucleic acids encoding a CD274 gene; (b) optionally, ligating one or more adaptors onto one or more nucleic acids from the plurality of nucleic acids; (c) optionally, amplifying nucleic acids from the plurality of nucleic acids; (d) optionally, capturing a plurality of nucleic acids corresponding to the CD274 gene; (e) sequencing, by a sequencer, the plurality of nucleic acids to obtain a plurality of sequence reads corresponding to the CD274 gene; (f) analyzing the plurality of sequence reads; and (g) based on the analysis, detecting one or more mutations in a CD274 gene. In some embodiments, the plurality of nucleic acids corresponding to the CD274 gene is captured from the amplified nucleic acids by hybridization with a bait molecule (para 29). Huang further teaches using computer processors for performing the method (para 56). Huang further teaches generating a report (para 293).
With respect to Claim 9, Huang teaches that cancer is metastatic.
With respect to Claim 10, Huang teaches the anticancer therapy comprises a small molecule inhibitor (para 32).
With respect to Claim 11, Huang teaches the therapy may be nivolumab (para 317).
With respect to Claim 12-13, Huang teaches the anticancer therapy of a kinase inhibitor in combination with another therapy including a chemotherapy (para 382).
With respect to Claims 15-16, Huang teaches analysis of a subject with a mutation and the CD274-PLGRKT fusion (see Table 9).
With respect to Claim 18-20, Huang teaches clonality is assessed (para 161).
With respect to Claim 21-22, the wherein clauses are merely inherent properties and do not require any additional method steps to be performed.
With respect to Claims 23-24, Huang teaches the sample may be a biopsy, blood, urine, or saliva (para 185).
With respect to Claim 25-27, Huang teaches the method includes enrichment, and PCR amplification.
With respect to Claim 28-29, Huan teaches using bait molecules that are about 10-30 nucleotides (para 45).
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.
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.
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) 3-5 is/are rejected under 35 U.S.C. 103 as being unpatentable over Lipson et al. (US 2016/0009785, January 14, 2016) in view of FusionGDB2 (PLGRKT-CD274 (FusionGDB2 ID: 65934).
Lipson teaches methods of detection fusion sequences and rearrangements. Lipson teaches methods of detection by generating a library comprising RNA or cDNA derived from RNA. The method comprises amplifying nucleic acids, capturing nucleic acids, sequencing and analyzing the presence of the fusion. Lipson further teaches using baits to capture target nucleic acids and sequencing (para 2236-2240).
Lipson does not teach analysis of fusion PLGRKT-CD274.
However FusionGDB2 (PLGRKT-CD274 (FusionGDB2 ID: 65934) is a fusion known to be associated with a variety of diseases including liver carcinoma, lymphoma, lung neoplasm and substance related disorders.
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention to have sequenced and detected the PLGRKT-CD274 fusion. The ordinary artisan would have been motivated to analyzed PLGRKT-CD274 in additional subjects to determine whether the subject had the presence or absence of PLGRKT-CD274.
Claim(s) 26-29 is/are rejected under 35 U.S.C. 103 as being unpatentable over The Cancer Genome Atlas Network (Nature, Vol. 517, pages 576-582, 2015) as evidenced by FusionGDB2 (PLGRKT-CD274 (FusionGDB2 ID: 65934) in view of Lipson et al. (US 2016/00096785, January 14, 2016).
The Cancer Genome Atlas Network teaches characterization of neck squamous cell carcinomas using Next generation sequencing.
FusionGDB2 (PLGRKT-CD274 (FusionGDB2 ID: 65934) teaches the rearrangement was identified in TCGA-CV-5443-01A sample. This was a sample from a 63 year old male for the TCGA program. Thus, TCGA-CV-5443-01A teaches all of the limitations of detecting knowledge of CD274.
The Cancer Genome Atlas Network does not teach analysis of fusions by enriching nucleic acid molecules using bait molecules.
However, Lipson teaches methods of detection fusion sequences and rearrangements. Lipson teaches methods of detection by generating a library comprising RNA or cDNA derived from RNA. The method comprises amplifying nucleic acids, capturing nucleic acids, sequencing and analyzing the presence of the fusion. Lipson further teaches using baits to capture target nucleic acids and sequencing (para 2236-2240).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention to have modified the next generation sequencing method of TCGA with other known methods for high throughput sequencing. The ordinary artisan would have recognized that the enrichment and bait capture methods of Lipson would allow more specific analysis of nucleic acid sequences of interest to be detected and measured.
Conclusion
No claims allowable over the art.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JEANINE ANNE GOLDBERG whose telephone number is (571)272-0743. The examiner can normally be reached Monday-Friday 6am-3:30pm.
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 Winston Shen can be reached on (571)272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JEANINE A GOLDBERG/Primary Examiner, Art Unit 1682
September 11, 2026
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