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 .
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 06/16/2026 and 06/17/2026 was filed after the mailing date of the Non-final Rejection on 03/17/2026. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Status of claims / Response to Amendment
This office action is in response to an amendment filed on June 16, 2026.
Claims 1-64 were previously pending. Applicant amended claims 1-2, 4, 21, 38-39; cancelled claims 14 and 40,
Claims 1-13, 15-39 and 41-64 are currently pending, with claims 41, 6-8, 10-12, 17, 19-20, 22-37, 41-43 and 45-64 withdrawn.
Claims 1-3, 5, 9, 13, 15-16, 18, 21, 38-39 and 44 are under consideration.
Applicant's submission of the amendment to specification obviated the previously presented objection.
All of the previously presented rejections have been withdrawn as either being addressed or obviated by the amendment of the claims, which introduces a new combination of elements that were not previously considered in the prior rejection (i.e., the amended claim 1 now require the split probes being "separately immobilized to a solid support at different positions"). Thus, the scope of the claims has been changed in a manner that were not considered in the previous rejections.
Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
This office action contains new grounds for rejection necessitated by amendment.
Priority
The priority date of the instant claims 1-3, 5, 9, 13, 15-16, 18, 21, 38-39 and 44 is 02/17/2021, filling date of the US provisional application NO. 63/150,095.
Claim Interpretation -- Updated
In evaluating the patentability of the claims presented in this application, claim terms have been given their broadest reasonable interpretation (BRI) consistent with the specification, as understood by one of ordinary skill in the art, as outlined in MPEP§ 2111.
Regarding claim 1, the claim has been amended to recite that the split probes "are separately immobilized to a solid support at different positions."
"Different positions" is interpreted here to mean different positions on the solid support. This interpretation is consistent with the specification at para. [0132]. See also FIG. 5.
Regarding claim 1, it recites an "enriching" step. The application's disclosure does not expressly define the term "enriching." The specification provides relevant descriptions pertaining to PCR enrichment using primers (e.g., [0166-0167]; [0176-0177]; [0182-0183]).
Accordingly, under BRI, the term "enriching" is understood as encompassing PCR.
Claim 1 recites the terms "partner DNA fragment" and "target DNA fragment," which are defined by the specification as follows:
"The term “target DNA fragment” refers to any nucleic acid molecule, polynucleotide sequence, or any fragment comprising a portion of a specific gene or genetic locus in the genomic DNA. The term “partner DNA fragment” refers to the fragment whose 3′ or 5′ sequence is joined to the 5′ or 3′ sequence of the “target DNA fragment.” The target DNA fragment or the partner DNA fragment includes an intact gene, an exon or intron, a regulatory sequence, or any region between genes. The DNA fragment at the 5′ end of the hybrid DNA fragment is referred to as “upstream DNA fragment”, and the DNA fragment at the 3′ end of the hybrid DNA fragment is referred to as “downstream DNA fragment."([0087])
Accordingly, under BRI and in view of the specification, "partner DNA fragment" and "target DNA fragment" are understood as joined DNA segments.
Claim 9 recites "DNA fragment joining boundary," which is defined by the specification as follows:
"The hybrid DNA fragment has a “DNA fragment joining boundary” which is the region where one DNA fragment is joined to another DNA fragment. For example, the regions that the partner DNA fragment is joined to the target DNA fragment, or the regions that the partner DNA fragment is joined to another DNA fragment or fusion junction." ([0088])
Accordingly, the term "DNA fragment joining boundary" is interpreted under BRI as encompassing a region of any range/size where two DNA fragments are joined, for example, a region within ± 1kb of a gene fusion junction site.
Claim Rejections - 35 USC § 103 -- New Grounds
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-3, 5, 9, 13 and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Mityaeva (Mityaeva et al. Analysis of Chromosome Translocations Involving MML by Hybridization with an Oligonucleotide Microarray. Molecular Biology 38, 376–382 (2004); doi.org/10.1023/B:MBIL.0000032208.13834.8b) , in view of
Rhodes (US20140315199A1 - Gene fusions and gene variants associated with cancer; Published on 2014-10-23) and
Greisman (Greisman et al.; Rapid high-resolution mapping of balanced chromosomal rearrangements on tiling CGH arrays. J Mol Diagn. 2011 Nov;13(6):621-33. doi: 10.1016/j.jmoldx.2011.07.005. Epub 2011 Sep 9. PMID: 21907824; PMCID: PMC3194053.)
A) Mityaeva teaches a method for analysis of chromosome translocation that combines reverse transcription–multiplex PCR and hybridization with an oligonucleotide microarray using split probes (Abstract).
Regarding claim 1, Mityaeva teaches a method for detecting a DNA fragment joining event, comprising:
(a) obtaining a DNA or a DNA from an extracted RNA in a sample (page 377, left-hand col, “RNA isolation and RT.”);
(b)enriching the DNA with a set of gene-specific oligonucleotides to obtain a target nucleic acid (page 377, left-hand col, “Standard and multiplex PCR”; right-hand col, lines 24-26, primers are designed based on specific gene sequences),
wherein the target nucleic acid is a joined DNA sequence comprising a partner DNA fragment and a target DNA fragment (Fig. 3, PCR products are chimeric genes, for example MLLex9/AF9(2)M);
(c) probing the target nucleic acid with a split probe set (page 377, right-hand col, “Hybridization of the labeled product with the microarray.”) comprising:
(i) a first split probe being complementary to a 3' region of the partner DNA fragment (Fig. 2-3, see MLLe9 probe, which is upstream of the MLL/AF9 gene fusion, this probe binding site, near the breakpoint is within the 3’ region of the MLL portion ),
a second split probe being complementary to-a 5' region of the target DNA fragment (Fig. 2-3, see AF9 (2) probe, which is downstream of the MLL/AF9 gene fusion, this probe binding site, near the breakpoint is within the 5’ region of the AF9 portion),
wherein a gap of the first and second split probes targeting sites on the target nucleic acid is within 0-80 bp;
wherein the first split probe, the second split probe are separately immobilized to a solid support at different positions (Fig. 2; page 379, left-hand col, para. 2, lines 10-12 “Oligonucleotide probes immobilized in gel pads of the microarray correspond to fragments of MLL and partner genes involved in rearrangements (Table 2). A scheme of oligonucleotide arrangement in the microarray is shown in Fig. 2a;”); and
(d) detecting a set of signals at the different positions that individually reflect
a hybridization between the partner DNA fragment and the first split probe,
a hybridization between the target DNA fragment and the second split probe (Fig. 2, see detection for MLLex9/AF9),
determining that:
(i) the partner DNA fragment is an upstream DNA fragment and the target DNA fragment is a downstream DNA fragment in the target nucleic acid (Fig. 2, see detection for MLLex9/AF9).
Mityaeva teaches detecting gene fusion events using split probes flanking the fusion site (Fig. 2; page, 379, right-hand col, lines 1-22). Although Mityaeva does not explicitly teach the length of gap between the first and second split probes targeting sites, this feature is obvious in view of the knowledge in the prior art.
A gap distance of 0-80 bp between the hybridization sites of two probes for fusion gene detection is well-known in the art.
Rhodes teaches probes that specifically recognize a gene fusion, the probes can flank a gene fusion and each bind a target sequence within 25 nucleotides of opposite sides of the one of the fusion breakpoints ([0140]), thus the gap between these probes flanking a gene fusion breakpoint is within 50 bp.
Greisman similarly teaches hybridization probes in an array for detection of chromosomal translocation and gene fusion, with median spacing of ∼60 nt between adjacent probes (Abstract; page 622, right-hand col, lines 20-21).
Accordingly, a person of ordinary skill in the art before the effective filing date of the claimed invention would have found it prima facie obvious for the hybridization probes used in Mityaeva’s method to have hybridization sites separated by a gap distance of 0-80 bp, as such spacing appears to have been well-known in hybridization probe design, particularly in the context of detecting fusion genes, as disclosed in Rhodes and Greisman.
This combination would have been obvious as it represents the KSR principle of predictable use of prior art elements according to a known method to yield predictable results. (See MPEP §2143).
B) Regarding claim 2, Mityaeva teaches gene-specific primers (page 377, left-hand col, “Standard and multiplex PCR”; right-hand col, lines 24-26, primers are designed based on specific gene sequences).
Regarding claim 3, Mityaeva teaches the DNA is amplified by multiplex PCR with at least two pairs of gene-specific primers in step (b) (page 377, left-hand col, “Standard and multiplex PCR”; Table 1).
Regarding claim 5, Mityaeva teaches at least two pairs of the gene-specific primers are designed to obtain the target nucleic acid from the partner DNA fragment as an upstream DNA fragment (Table 1, 1st step and second step multiplex primer pairs for MLL/AF9 rearrangement, with MLL being the upstream DNA fragment).
Regarding claim 9, Rhodes teaches probes target within a distance of 0-40bp from a DNA fragment joining boundary ([0140] “a detector probe that binds to either side of a breakpoint in a gene fusion … detector probe binds to a target sequence in the human genome within … 25 nucleotides of one of the fusion breakpoints”).
Regarding claim 13, Mityaeva teaches probe length is 10-60 bp (Table 2).
Regarding claim 21, Mityaeva teaches fluorescent signal (page 378, left-hand col, para 2).
Claims 15-16, 18, 38-39 and 44 are rejected under 35 U.S.C. 103 as being unpatentable over Mityaeva, in view of Rhodes with Greisman, as applied to claim 1 above and further in view of Amatu (Amatu et al., NTRK gene fusions as novel targets of cancer therapy across multiple tumour types. ESMO Open. 2016 Mar 18;1(2):e000023. doi: 10.1136/esmoopen-2015-000023. PMID: 27843590; PMCID: PMC5070277; cited in prior Office Action).
The teachings of Mityaeva, Rhodes and Greisman are recited above and applied as for base claim 1.
Regarding claims 15, 16, and 18, Applicant elected ETV6, as partner DNA fragment sequence; and NTRK3 as target DNA fragment sequence. Accordingly, the DNA fragment joining event (e.g., gene fusion) in claim 18 corresponds to ETV6-NTRK3.
Mityaeva teaches a method for analysis of analyzing gene fusions using split probes (Abstract).
Although Mityaeva does not explicitly disclose detecting the specific gene fusion ETV6-NTRK3, a person of ordinary skill in the art would have found it obvious to apply the fusion detection method of Mityaeva to detect ETV6-NTRK3, because ETV6-NTRK3 fusion is well-known and have been widely studied for clinical applications, this is supported by Amatu.
As extensively discussed in Amatu, which is a review article addressing ETV6-NTRK3 fusion across multiple cancer types (Table 1, ETV6-NTRK3) and therapeutic strategies targeting such fusions (Table 2), the ETV6-NTRK3 fusion is well-known and have been widely studied (see Table 1). Amatu further teaches that ETV6-NTRK3 fusion, which is the most studied NTRK3 fusion, is among the fusion targets investigated in several cancer therapies undergoing clinical evaluation (see Tables 1 and 2). Therefore, the prior art demonstrates strong interest in detecting and monitoring ETV6-NTRK3 fusion for clinical applications, such as patient stratification and monitoring therapeutic response in clinical trials directed to such gene fusions.
Thus, in view of the above, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to apply the gene fusion detection methods of Mityaeva to detect the ETV6-NTRK3 fusion disclosed in Amatu.
This combination would have been obvious as it represents the KSR principle of predictable use of prior art elements (i.e., known ETV6-NTRK3 fusion) according to a known method (i.e., gene fusion detection method in Mityaeva, in view of Rhodes with Greisman) to yield predictable results. (See MPEP §2143).
B) Regarding claim 38, Amatu teaches administering to cancer patient: a therapeutically effective amount of an NTRK inhibitor (Table 2, in clinical trials therapeutically effective amount of drugs with known inhibitory activity of NTRK-related kinases are administered to cancer patients, see Entrectinib for example, which is identified in the instant specification as an NTRK inhibitor, see spec [0139]).
Regarding claim 39, Amatu teaches ETV6-NTRK3 fusion (Table 1).
Regarding claim 44, Amatu teaches carcinoma (Table 1, ETV6-NTRK3, Ductal carcinoma).
Prior Art
Below are relevant prior art not used in rejection but pertinent to the claims or disclosure.
Other prior art also teach gene fusion detection methods comprising enriching DNA with a set of oligonucleotides and probing enriched target nucleic acid with split probes:
Skotheim et al., A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis. Mol Cancer. 2009 Jan 19;8:5. doi: 10.1186/1476-4598-8-5. PMID: 19152679; PMCID: PMC2633275;
Giusiano et al.; Development of a biochip-based assay integrated in a global strategy for identification of fusion transcripts in acute myeloid leukemia: a work flow for acute myeloid leukemia diagnosis. Int J Lab Hematol. 2010 Aug 1;32(4):398-409. doi: 10.1111/j.1751-553X.2009.01201.x. Epub 2009 Nov 23. PMID: 19930410;
Xiong et al., A Pipeline with Multiplex Reverse Transcription Polymerase Chain Reaction and Microarray for Screening of Chromosomal Translocations in Leukemia, BioMed Research International, 2013, 135086, 13 pages, 2013. https://doi.org/10.1155/2013/135086;
Nasedkina et al. Biological microchip for establishing the structure of fusion transcripts involving MLL in children with acute leukemia. Mol Biol 50, 852–859 (2016). https://doi.org/10.1134/S0026893316060145;
Qing et al.; A sensitive array-based assay for identifying multiple TMPRSS2:ERG fusion gene variants, Nucleic Acids Research, Volume 36, Issue 20, 1 November 2008, Page e130, doi.org/10.1093/nar/gkn585;
Maroc et al.; A diagnostic biochip for the comprehensive analysis of MLL translocations in acute leukemia. Leukemia 18, 1522–1530 (2004). doi.org/10.1038/sj.leu.2403439;
Chun et al. ; Identification of leukemia-specific fusion gene transcripts with a novel oligonucleotide array. Mol Diagn Ther. 2007;11(1):21-8. doi: 10.1007/BF03256220. PMID: 17286448.
Conclusion
No claims are allowed.
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.
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/TIAN NMN YU/Examiner , Art Unit 1681 /AARON A PRIEST/Primary Examiner, Art Unit 1681
1 Amended claim 4 has been withdrawn as being drawn to nonelected species G) a first split probe being complementary to the 3' end of a partner DNA fragment and a second split probe being complementary to the 5' end of a target DNA fragment and a third split probe being complementary to a third DNA fragment, within the "Species of split probe" grouping. See Requirement for Restriction/Election - 12/22/2025.
In the Reply filed on February 13, 2026, Applicant elected:
Species D) a first split probe being complementary to the 3' end of a partner DNA fragment and a second split probe being complementary to the 5' end of a target DNA fragment.
Accordingly, the amended claim 4 has been withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention.
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