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 .
Claims 1-3, 6-11, and 14-15 are pending and currently under examination. Claims 4-5, 12-13, and 16-22 are cancelled. Claim 1 is amended.
Response to Amendment
The Amendment filed 1/23/26 has been entered. Claims 1-3, 6-11, and 14-15 are pending.
Response to Arguments
Applicant’s arguments, see pages 4-7, filed 1/23/26, with respect to the rejections of claims 1-3, 6-11, and 14-15 under 35 USC 103 have been fully considered and are found persuasive. Therefore, the rejections documented in the Non-Final mailed 11/5/25 have been withdrawn. However, upon further consideration, new grounds of rejections necessitated by claim amendments are made in this Final Office Action.
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.
Claims 1-3, 6-11, and 14-15 are rejected under 35 U.S.C. 103 as being unpatentable over Lowman et al. (2019; FOR citation N in PTO-892 filed on 3/24/25; WO 2019/046817 A1) in view of Pel et al. (2018; NPL citation 5 in IDS filed 10/4/22; “Rapid and highly-specific generation of targeted DNA sequencing libraries enabled by linking capture probes with universal primers”; PLoS One. 2018 Dec 5;13(12):e0208283. doi: 10.1371/journal.pone.0208283), Pugh et al. (2019; US Patent Document citation A in PTO-892 filed on 3/24/25; US 2019/0390273 A1), and Montagne et al. (2018; NPL citation U in PTO-892 filed 11/5/25; "Ultra-Efficient Short Read Sequencing of Immune Receptor Repertoires"; bioRxiv preprint doi: https://doi.org/10.1101/494062; this version posted December 13, 2018).
This new 103 rejection is necessitated by claim amendments filed 1/23/26 and addresses the amended limitations “
(i) Relevant to claim 1, Lowman et al. teaches “methods, compositions, kits, and systems useful in the determination and evaluation of the immune repertoire using genomic DNA from a biological sample” (Abstract).
This teaching reads on claim 1 A method for profiling adaptive immune systems, wherein the Lowman et al. “determination and evaluation of the immune repertoire” reads on the instant profiling adaptive immune systems.
Further relevant to claim 1, Lowman et al. teaches “target-specific primer panels” (Abstract) and that “In certain embodiments, methods of the invention comprise use of a biological sample selected from… lymphocytes…” (page 34, paragraph 00100), reading on nucleic acid fragments from one or more lymphocytes.
Further relevant to claim 1, the Lowman et al. primers are “directed to a portion of a V gene framework region and a portion of a J gene of target immune receptor genes selected from the group consisting of TCR [T cell receptor] beta, TCR alpha, TCR gamma, TCR delta, immunoglobulin heavy chain, immunoglobulin light chain lambda, and immunoglobulin light chain kappa” (page 9, paragraph 0032). Lowman et al. teaches that “In some embodiments, the forward primer and the reverse primer are capable of hybridizing to opposite strands of a nucleic acid duplex. Optionally, the forward primer primes synthesis of a first nucleic acid strand, and the reverse primer primes synthesis of a second nucleic acid strand, wherein the first and second strands are substantially complementary to each other, or can hybridize to form a double-stranded nucleic acid molecule” (page 49, paragraph 00145).
These teachings read on claim 1 exposing the nucleic acid fragments to (i) a plurality of forward linked capture probes each comprising… a forward target probe that anneals to a variable (V) gene region of a target gene, and (ii) a plurality of reverse linked capture probes each comprising… a reverse target probe that anneals to a joining (J) gene region of the target gene, wherein the target gene is selected from the group consisting of a T cell receptor chain gene, an immunoglobulin heavy chain gene, and an immunoglobulin light chain gene, wherein the exposing step occurs under conditions that require binding of the forward or reverse target probe.
Relevant to claims 9-11, Lowman et al. page 34, paragraph 00100 teaches that “In some embodiments, the biological sample comprises cells selected from the group consisting of… T cells, B cells”. Additionally, Lowman et al. Abstract teaches that their “target-specific primer panels provide for the effective amplification of sequences of T cell receptor and/or B cell receptor chains”.
These teachings read on claim 9 wherein the one or more lymphocytes are T cells; claim 10 wherein the one or more lymphocytes are B cells; and claim 11 wherein the one or more lymphocytes comprise both B cells and T cells.
Relevant to claim 15, Lowman et al. teaches that “In some embodiments, the sample comprises cDNA, RNA… The term [sample] also includes any isolated nucleic acid sample such as genomic DNA” (page 48, paragraph 00143).
This teaching reads on claim 15 the nucleic acid fragments comprise one or more of DNA, RNA, or cDNA.
(ii) Lowman et al. is silent to the limitations of attaching universal priming sites…; a copy of a universal primer linked to a… target probe; extending the copies of the universal primer to produce copies of the target gene; sequencing the copy to profile a subject’s adaptive immune system (claim 1) and the attaching step comprises ligation… (claim 14). However, these limitations were known in the prior art and taught by Pel et al.
Relevant to claims 1 and 14, Pel et al. teaches “Rapid and highly-specific generation of targeted DNA sequencing libraries enabled by linking capture probes with universal primers” (Title). As seen in Pel et al. Fig. 1 and described within the figure caption, Fig. 1 (a) depicts “Custom adapters (i) are ligated to template DNA and the resulting product is amplified with universal primers”.
These teachings read on claim 1 attaching universal priming sites… and claim 14 the attaching step comprises ligation.
Further relevant to claim 1, Pel et al. Fig. 1 (b) and caption teach “Target regions are selectively amplified using custom probe-dependent primers (PDPs) (ii) which contain a recognition sequence (dark grey) … and are linked to an oligo containing a universal priming sequence for the first target capture PCR reaction (tcPCR1).”
The Pel et al. “recognition sequence” corresponds to the instant target probe that is linked to the “universal priming sequence” (instant universal primer). This teaching reads on claim 1 a copy of a universal primer linked to a… target probe.
Further relevant to claim 1, Pel et al. Fig. 1 (b) also depicts that the exposing step occurs under conditions that require binding of the… target probe to permit the copy of the universal primer that is linked to that… target probe to bind to the universal priming site. This is supported by the Pel et al. page 3, paragraph 1 of Results section “Linked target capture concept” explanation that “When bound to their targets, the probes bring the universal primer into close proximity with the universal priming site on the template”.
Further relevant to claim 1, Pel et al. teaches that this methodology results in “increasing the reaction rate of primer binding and initiating polymerase extension. The polymerase displaces or digests the probe portion of the PDP to make a copy of the entire target template” (page 3, paragraph 1 of Results section “Linked target capture concept”).
This teaching reads on claim 1 extending the copies of the universal primer to produce copies of the target gene.
Further relevant to claim 1, Pel et al. teaches that “To create sequencer-compatible libraries, the second tcPCR integrates the full Illumina P5 and P7 sequences into the universal primer portion of the PDPs [Probe-Dependent Primers]” (page 3, paragraph 1 of Results section “Linked target capture concept”).
This teaching reads on claim 1 sequencing the copy.
(iii) Lowman et al. and Pel et al. are silent to capture probes that overlap with each other (claim 1), targeting all V gene regions (claim 2) or J gene regions (claim 3); a plurality of subregions (claim 6); and subregion overlaps (claims 7-8). However, these limitations were known in the prior art and taught by Pugh et al.
Pugh et al. teaches “a method of capturing a population of T-Cell receptor and/or immunoglobulin sequences with variable regions within a patient sample… using a collection of nucleic acid hybrid capture probes, wherein each capture probe is designed to hybridize to a known V gene segment and/or a J gene segment within the T cell receptor and/or immunoglobulin genomic loci” (Abstract).
Relevant to claim 1, Pugh et al. page 13, paragraph 0204 teaches “Primer set physicochemical characteristics were evaluated using the IDT OligoAnalyzer Tool (v 3.1); Clustal W (53 alignments were used to identify significant primer sequence overlaps (Clustal W alignments note significant overlap of the TRGJ1 and TRGJ2 primers. This overlap was considered acceptable in order to define which of the TRGJ1 and TRGJ2 genes were present (given the presence of 5' end non-homology).”
This teaching reads on claim 1 capture probes that overlap with each other.
Relevant to claims 2-3, Pugh et al. page 19, paragraph 0309 teaches that “The target capture panel consists of 598 probes (IDT) targeting the 3’ and 5’ 100 bp of all TR [T-cell receptor] V gene regions” (claim 2), “and 95 probes targeting the 5’ 100 bp of all TR J gene regions” (claim 3).
This teaching reads on the plurality of linked capture probes comprise capture probes targeting all V gene regions (claim 2) and all J gene regions (claim 3).
Relevant to claim 6, Pugh et al. page 2, paragraph 0016 teaches “using a collection of nucleic acid hybrid capture probes, wherein each capture probe is designed to hybridize to a known V gene segment and/or a J gene segment within the T cell receptor and/or immunoglobulin genomic loci”.
This teaching reads on claim 6 a plurality of subregions within the V region and the J region.
Relevant to claim 7, Pugh et al. pages 2-3, paragraphs 0017-0024 outline a method of identifying “a junction nucleotide sequence comprising at least the junction between the V gene segment and the J gene segment”, wherein the “junction” indicates overlaps of the V and J gene segments.
Taken with the above teaching of “V gene segment and/or a J gene segment” relevant to claim 6, Pugh et al. reads on claim 7 limitation of each of the plurality of subregions overlaps with another of the plurality of subregions.
Relevant to claim 8, Pugh et al. page 3, paragraph 0024 teaches that “the junction nucleotide sequence [comprises] between 18 bp and 140 bp”, reading on each of the plurality of subregions overlaps with another of the plurality of subregions by 5 or more bases.
(iv) Lowman et al., Pel et al., and Pugh et al. are silent to universal bases (claim 1). However, these limitations were known in the prior art and taught by Montagne et al.
Montagne et al. teaches “Ultra-Efficient Short Read Sequencing of Immune Receptor Repertoires” (Title).
Relevant to claim 1, Montagne et al. teaches “By designing maximally compact primer sets and a streamlined workflow, we have essentially eliminated PCR amplification bias and dramatically reduced assay cost, enabling CDR3 analysis via single-end, short-read (100 nt) sequencing” (page 3, paragraph 1).
Further relevant to claim 1, Montagne et al. teaches “We developed a heuristic algorithm to automate the design of three candidate sets of primers, each targeting the 47 distinct FR3 3' 20-mers (Fig S1): one primer set lacks any universal bases or mismatches (‘Full’ set), one primer set lacks universal bases but allows a single mismatch to occur (‘1MM’ set), and one primer set contains parsimonious incorporation of up to 3 universal (inosine) bases and allows one mismatch (‘Compact’ set)” (page 4, paragraph 2).
This Montagne et al. teaching establishes that universal bases have been used in primer designs directed towards immune receptor profiling.
(v) It would have been prima facie obvious to include the Pel et al. linked capture probes, Pugh et al. overlapping regions, and Montagne et al. universal bases within the Lowman et al. method of profiling adaptive immune systems to profile a subject’s adaptive immune system. It is noted that Lowman et al., Pel et al., Pugh et al., and Montagne et al. are analogous disclosures to the instant method of amplification-based profiling.
The skilled artisan would recognize that the Lowman et al. immune system profiling primers can be modified to include the Pel et al. linked capture probe components. Lowman et al. teaches that “universal adapter/primer sequences described and known in the art… can be used in conjunction with the methods and compositions provided herein and the resultant amplicons sequenced using the associated analysis platform” (page 13, paragraph 0044). As the Lowman et al. method is amenable to this modification, the skilled artisan would consider it obvious to include the Pel et al. linked capture probe components. Additionally, Pel et al. Materials and methods section “PDP design and conjugation” teaches that “Capture probes were designed to cover portions of 35 cancer-related genes”, indicating that the probes are amenable to gene or region-specific customization dependent on the intended target.
The skilled artisan would be motivated to use the Pel et al. capture probes within the Lowman et al. methodology because Pel et al. teaches that “sequencing libraries were prepared in less than eight hours from extracted DNA to loaded sequencer, demonstrating that LTC [Linked Target Capture] holds promise as a broadly applicable tool for rapid, cost-effective and high-performance targeted sequencing” (Abstract).
Although Lowman et al. is silent to the Pugh et al. overlapping regions, it would have been prima facie obvious to the skilled artisan to include the Pugh et al. methodology within the Pel et al.-modified Lowman et al. methodology. Pugh et al. teaches that the T-cell receptor “specificity, and indeed the vast array of potential antigenic epitopes that may be recognized by the population of T-cells on the whole, is afforded by (1) the number of TR [T-cell receptor] encoding regions of a given T-cell receptor’s genes as present in the germline; and (2) the intrinsic capacity of the TR gene loci to undergo somatic re-arrangement” (page 1, paragraph 0005). Thus, the skilled artisan would be motivated to emulate Pugh et al.’s expansive probe panel in order to effectively capture the multitude of T-cell receptor encoding regions possibly undergoing expansive re-arrangements. To this end, Pugh et al. teaches that they “have developed a hybrid-capture method that recovers rearranged sequences of T-cell receptor (TCR) chains from all four classes (alpha, beta, gamma, and delta loci) in a single reaction from an Illumina sequencing library. We use this method to describe the TCR V(D)J repertoire” (page 6, paragraph 0091).
The skilled artisan would be motivated to use the Montagne et al. universal bases within the Lowman et al. methodology. Montagne et al. Abstract teaches that “Immune receptor repertoire (IRR) sequencing has facilitated the unprecedented analysis of adaptive immune responses. Current methods for quantitative IRR analysis, however, are limited by protocol complexity, cost, or both. Here we present Framework Region 3 AmplifiKation sequencing (“FR3AK-seq"), a multiplex PCR-based methodology for the ultra-efficient analysis of IRRs. We demonstrate that this approach is sensitive and quantitative, and generates results comparable to the current industry standard. In addition, we establish its utility for the streamlined and cost-effective analysis of large sample collections. We anticipate that FR3AK-seq will enable the routine and extensive analysis of IRRs, significantly increasing the frequency, scope, and power of such studies.”
The Montagne et al. universal bases are components of their FR3AK-seq approach, which provides for multiple applications and advantages compared to current industry standards. Thus, the skilled artisan would be motivated to include the universal bases within the modified Lowman et al. methodology because of the Montagne et al.-taught advantages.
The Lowman et al. profiling method would benefit from the inclusion of Pel et al. linked target capture probes, Pugh et al. overlapping regions, and Montagne et al. universal bases; the skilled artisan would have a reasonable expectation of success based on the disclosures of Lowman et al. in view of Pel et al., Pugh et al., and Montagne et al., as discussed in the preceding paragraphs.
Conclusion
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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/SARAH JANE KENNEDY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682