DETAILED ACTION
Status of the Claims
Claims 61-69 are currently pending and are examined herein.
The following Office Action is in response to Applicant’s communication dated 01/07/2026. Rejection(s) and/or objection(s) not reiterated from previous office actions are hereby withdrawn. The following rejection(s) and/or objection(s) are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
The present application is being examined under the pre-AIA first to invent provisions.
Response to Restriction Requirement
Applicant’s election without traverse of Group I (claims 61-69) in the reply filed on 09/24/2025 is acknowledged.
Drawings
The objection to the drawings because the “Replacement Drawings” filed 05/02/2022 allegedly did not align with the Brief Description of the Drawings in the specification is withdrawn in light of persuasive arguments presented by Applicant in the 01/07/2026 response.
Specification
The objection to the specification because the Brief Description of the Drawings on pages 9-10 allegedly did not align with the Replacement Drawings filed on 05/02/2022 is withdrawn in light of persuasive arguments presented by Applicant in the 01/07/2026 response.
Withdrawn Claim Objections
The objection to claims 65 and 68 because they did not end with a period is withdrawn in light of amendments made by Applicant to the claims in the response of 01/07/2026.
New Claim Objections
Necessitated by Amendments
Claim 65 is objected to as being dependent upon a rejected base claim, but would be free from the prior art if rewritten in independent form including all of the limitations of the base claim and any intervening claims. Appropriate correction is required.
New Claim Rejections - 35 USC § 112, 2nd Paragraph
Necessitated by Amendments
The following is a quotation of 35 U.S.C. 112(b):
(B) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 61-69 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.
Claim 61 has been newly amended to recite in step (c) that “sequence Y’ is complementary to sequence YU”, however, there is no sequence YU and therefore the claim lacks proper antecedent basis for this new limitation. Accordingly, the metes and bounds of the claim are unascertainable.
This appears to be a typographical error, wherein the “U” was inadvertently added. Applicant could overcome this rejection by amending the limitation back to “sequence Y”.
Claims 62-69 depend from claim 61 and are therefore similarly rejected.
As per MPEP 2173: It is of utmost importance that patents issue with definite claims that clearly and precisely inform persons skilled in the art of the boundaries of protected subject matter. Therefore, claims that do not meet this standard must be rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph as indefinite. Further, as per MPEP 2173.02: If the language of the claim is such that a person of ordinary skill in the art could not interpret the metes and bounds of the claim so as to understand how to avoid infringement, a rejection of the claim under 35 U.S.C. 112, second paragraph, would be appropriate. As currently written, the metes and bounds of the rejected claims are unascertainable for the reasons set forth above, thus the above claim(s) and all dependent claims are rejected under 35 USC 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph.
Modified Claim Rejections - 35 USC § 103
Necessitated by Amendments
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.
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims under 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of 35 U.S.C. 103(c) and potential 35 U.S.C. 102(e), (f) or (g) prior art under 35 U.S.C. 103(a).
Amorese et al. and Illumina
Claims 61-64 and 66-69 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Amorese et al. (U.S. PGPub 2013/0231253 A1, of record) in view of Illumina (Illumina Sequencing Technology technical bulletin, 2010).
Regarding claim 61(in part), Amorese discloses a method of enriching a plurality of different target polynucleotides in a sample (e.g., as per Fig. 1 and throughout) comprising:
(a) joining an adapter oligonucleotide to each of the target polynucleotides (e.g., which can be cDNA as per [0044]-[0047]), wherein the adapter oligonucleotide comprises sequence Y (e.g., appending a “first adaptor” or “forward adaptor” to the 5’ ends, as per [0028]-[0029]);
(b) hybridizing a plurality of different oligonucleotide primers to the adapted target polynucleotides, wherein each oligonucleotide primer comprises sequence Z and sequence W; wherein sequence Z is common among all oligonucleotide primers, and further wherein sequence W is different for each different oligonucleotide primer, is positioned at the 3' end of each oligonucleotide primer (e.g., as per [0030], which states, in part:
“In a preferred embodiment, the one or more oligonucleotides that comprise sequence complementary to different or distinct target nucleic acid sequences of interest further comprise the same second adaptor sequence. In one embodiment, the sequence complementary to the target sequence of interest can be at the 3'end of the oligonucleotide and the second adaptor sequence can be at the 5'end of the oligonucleotide. In a preferred embodiment, the second adaptor sequence is non-complementary to the target nucleic acid sequence of interest. In this manner, the second adaptor sequence serves as a tail.”
), and is complementary to a sequence comprising a causal genetic variant or a sequence within 200 nucleotides of a causal genetic variant (e.g., the 3’ end of the oligonucleotide anneals to a sequence termed a “region of interest”, which can be for “analysis of SNPs or other disease markers” as per [0070] and/or “polymorphisms, or alleles, can be associated with diseases” as per [0075]); and
(c) in an extension reaction, extending the oligonucleotide primers along the adapted target polynucleotides to produce extended primers comprising sequence Z and sequence Y', wherein sequence Y' is complementary to sequence Y (e.g., primer extension as per [0031]), wherein each oligonucleotide primer comprises a first binding partner (e.g., “the first adaptor and/or the second adaptor sequence can comprise flow cell sequences which can be used for sequencing with the sequencing method developed by Illumina and described herein” as per para [0032]).
Amorese further states in para [0071] that the resulting double stranded fragment polynucleotides can produce amplified nucleic acid sequences tagged at one or both ends, then denatured and the single-stranded polynucleotides are randomly attached to the inside surface of flow-cell channels, followed by solid-phase bridge amplification to produce dense clusters of double-stranded DNA, however, the reference is silent as to some of the precise details involved in such Illumina bridge amplification and sequencing, as set forth in claims 61(d)-(e) and 67-68.
Illumina discloses steps of exposing the extended primers to a flow cell plate surface comprising a second binding partner that binds to the first binding partner (e.g., as per Figure 3: Attach DNA to Surfaces of Illumina), thereby purifying the extended primers away from one or more components of the extension reaction (e.g., since moieties without the first binding partner will not hybridize to the second binding partner of the flow cell). This “first binding partner” added to the enriched DNA above and the “second binding partner” may also correspond to the adaptor sequence Y/Y’ and the immobilized “dense lawn of primers” as shown in Figure 3: Attach DNA to Surfaces of Illumina), respectively.
Illumina then discloses exponentially amplifying the purified extension products by bridge amplification to produce double-stranded bridge polynucleotides using a pair of amplification primers comprising the immobilized primers of the flow cell (e.g., as per Figures 4-5 of Illumina). Further, Illumina discloses cleaving one strand of each of the double-stranded bridge polynucleotides, and denaturing the cleaved bridge polynucleotide to produce a free single-stranded polynucleotide comprising a target sequence attached to the solid surface (e.g., as per Figures 6-7 of Illumina).
Regarding claim 62, Amorese discloses the above method, wherein sequences W, Y, and Z are different sequences and comprise 5 or more nucleotides each (e.g., Z is the sequence common to the adaptors, W varies by the region of interest, and Y is the flow cell adaptor, as described above).
Regarding claim 66, Amorese discloses the above method, wherein the target polynucleotides comprise fragmented polynucleotides that have a median length between about 200 and about 1000 base pairs (e.g., as per [0024]), and wherein the fragmented polynucleotides are treated to produce blunt ends or to have a defined overhang prior to step (a), such as an overhang consisting of an adenine (e.g., as per [0024]).
Regarding claims 67-68, Illumina discloses sequencing the target sequence by hybridizing a sequencing primer to a bound template, extending the sequencing primer, and identifying nucleotides added by extension of the sequencing primer (e.g., as per Figures 8-12 of Illumina).
Regarding claim 69, Amorese discloses the above method, wherein the plurality of different oligonucleotide primers further comprises additional oligonucleotide primers comprising sequence Z and sequence W, wherein sequence W is different for each different additional oligonucleotide primer, is at the 3' end of each additional oligonucleotide primer, and is complementary to a sequence comprising a non-subject sequence or a sequence within 200 nucleotides of a non-subject sequence (e.g., as per Example 1).
It would have been prima facie obvious to a person of ordinary skill in the art at the time the invention was made to subject the amplified samples of Amorese to Illumina bridge amplification and sequencing as per Illumina Sequencing Technology technical bulletin. One of ordinary skill in the art would have been motivated to do so since Amorese explicitly discloses in several locations the use of Illumina sequencing, lacking only in the specific details of the technology, which are supplied by Illumina.
One of ordinary skill in the art would have had a reasonable expectation of success as of the time of the invention in modifying the references to arrive at the claimed invention since at the time Illumina sequencing (including sample preparation) was routine and available as a service and/or with the use of commercially available kits.
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Response to Arguments
The 01/07/2026 remarks argue: not all elements are taught.
Applicant's arguments have been fully considered but they are not persuasive for at least the following reasons.
In response, it is noted that the rejection herein has been modified to address the amendments recited in the arguments in the 01/07/2026 remarks.
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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JEREMY FLINDERS whose telephone number is (571)270-1022. The examiner can normally be reached M-F 10-6:00 EST.
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/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684
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