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 .
Claim Status
Claims 1-227 are cancelled (6/14/2024). Claims 228-248 are new (6/14/2024). No new matter was added. Thus, claims 228-248 are under examination.
Priority
Claims 228-248 are given a priority date of 12/5/2014, the filing date of US Provisional 62088457.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Information Disclosure Statement from 6/14/2024 is considered.
Specification
The disclosure is objected to because of the following informalities:
The use of the term Agilent Technologies, Inc (p. 129, 201), QIAGEN (p. 190 and used throughout the Specification), character issue not translating on p. 190 (lines 3-4), Integrated DNA Technologies (p. 192), New England BioLabs (p. 192), Illumina (p. 195-196), AMPureXP (p. 196), Invitrogen (p. 205), which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (p. 209, NCBI). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Rejections - 35 USC § 103
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.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 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 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) 228-248 are rejected under 35 U.S.C. 103 as being unpatentable over Robins et al., (US PGPub 2010/0330571 A1, published 12/30/2010), in view of Shojaei et al. (“Unusually long germline DH genes contribute to large sized CDR3H in bovine antibodies”, Molecular Immunology, published 2003).
Regarding claims 228-231, Robins teaches a method of measuring immunocompetence via providing a means for assessing the effects of diseases or conditions that compromise the immune system and of therapies aimed to reconstitute it. This method is based on quantifying T-cell diversity by calculating the number of diverse T-cell receptor (TCR) beta chain variable regions from blood cells (Abstract). Further, Robins teaches that an embodiment of the invention is the method, wherein the diversity of at least two samples of genomic DNA are compared. wherein one sample of genomic DNA is from a patient and the other sample is from a normal subject or wherein the two samples of genomic DNA are from the same patient at different times during treatment (Paragraph 41, lines 1-10). Robins also teaches that recent advances in high-throughput DNA sequencing technology have made possible significantly deeper sequencing than capillary-based technologies where a complex library of template molecules carrying universal PCR adapter sequences at each end is hybridized to a lawn of complementary oligonucleotides immobilized on a solid surface and solid phase PCR is utilized to amplify the hybridized library, resulting in millions of template clusters on the surface, each comprising
multiple (-1,000) identical copies of a single DNA molecule from the original library (Paragraph 47, lines 1-8). Specifically, Robins teaches that 30-54 bp interval in the molecules in each cluster is sequenced using reversible determination chemistry, to permit simultaneous sequencing
from genomic DNA of the rearranged TCR~ chain CDR3 regions carried in millions of T cells and this approach enables direct sequencing of a significant fraction of the uniquely rearranged TCR~ CDR3 regions in populations of a~ T cells, which thereby permits estimation of the relative frequency of each CDR3 sequence in the population (Paragraph 47, lines 10-20). Robins further teaches that alternatively, total nucleic acid can be isolated from
cells, including both genomic DNA and mRNA and if diversity is to be measured from mRNA in the nucleic acid extract, the mRNA must be converted to cDNA prior to measurement (Paragraph 55, lines 1-5).
Also, Robins teaches that the assay technology uses two pools of primers to
provide for a highly multiplexed PCR reaction where the "forward” pool has a primer specific to each V segment in the gene (several primers targeting a highly conserved region are used,
to simultaneously capture many V segments) and the "reverse" pool primers anneal to a conserved sequence in the joining ("J") segment where the amplified segment pool includes adequate sequence to identify each J segment and also to allow for a J-segment-specific primer to anneal for resequencing and this enables direct observation of a large fraction of the somatic
rearrangements present in an individual, and this in tum enables rapid comparison of the TCR repertoire in individuals with an autoimmune disorder (or other target disease indication)
against the TCR repertoire of controls (Paragraph 50, lines 1-20). Robins additionally teaches that B cells and T cells can be obtained from a variety of tissue samples including marrow, thymus, lymph glands, peripheral tissues and blood, but peripheral blood is most easily accessed and peripheral blood samples are obtained by phlebotomy from subjects (Paragraph 54, lines 1-5).
Regarding claim 232, Robins teaches that TCR and Ig genes generate extensive diversity through somatic mutation and that genes contain hypervariable complementarity-determining regions (CDRs) (Paragraph 42, lines 1-5).
Regarding claims 233-245, Robins teaches A multiplex PCR system is used to amplify rearranged TCR loci from genomic DNA, preferably from a CDR3 region, more preferably from a TCRa, TCRy or TCR or CDR3 region, most preferably from a TCR~ CDR3 region and in general, a multiplex PCR system may use at least 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25, preferably 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, or 39, most preferably 40, 41, 42, 43, 44, or 45 forward primers, in which each forward primer is specific to a sequence corresponding
to one or more TRB V region segments shown in SEQ ID NOS:114-248; and at least 3, 4, 5, 6, or7,preferably 8, 9, 10, 11, 12 or 13 reverse primers, in which each reverse primer is specific to a sequence corresponding to one or more TRB J region segments shown in SEQ ID NOS:249-261 and most preferably, there is a J segment primer for every J segment (Paragraphs 57-58). Further, Robins teaches that preferably, the primers are designed not to cross an intron/exon boundary and the forward primers must preferably anneal to the V segments in a region of relatively strong
sequence conservation between V segments so as to maximize the conservation of sequence among these primers and accordingly, this minimizes the potential for differential annealing properties of each primer, and so that the amplified region between V and J primers contains sufficient TCR V sequence information to identify the specific V gene segment used (Paragraph 59). Robins also teaches that preferably, the J segment primers hybridize with a conserved element of the J segment, and have similar annealing strength and most preferably, all J segment primers anneal to the same conserved framework region motif where the forward and reverse primers are both preferably modified at the 5' end with the universal forward primer sequence compatible with a DNA sequencer (Paragraph 60, lines 1-5).
Robins also teaches that another aspect of the invention is a composition comprising:
a multiplicity of V segment primers, wherein each V segment primer comprises a sequence that is complementary to a single functional V segment or a small family of V segments; and multiplicity of J segment primers, wherein each J segment primer comprises a sequence that is complementary to a J segment; wherein the V segment and J segment primers permit
amplification of antibody light chain (IGL) VL region by a multiplex polymerase chain reaction (PCR) to produce a multiplicity of amplified DNA molecules sufficient to quantify the diversity of antibody light chain genes (Paragraphs 23-26).
Additionally, Robins teaches that The TCRs expressed by a~ T cells, which primarily
recognize peptide antigens presented by major histocompatibility complex (MHC) class I and II molecules, are heterodimeric proteins consisting of two transmembrane polypeptide chains (a and~), each containing one variable and one constant domain where the peptide specificity of a~ T cells is in large part determined by the amino acid sequence encoded in the third complementarity-determining region (CDR3) loops of the a and ~ chain variable domains and the CDR3 regions of the~ and a chains are formed by recombination between noncontiguous variable (V 13), diversity (D13), and joining (J 13) gene segments in the ~ chain locus, and
between analogous Va and Ja gene segments in a chain locus, respectively, where the existence of multiple such gene segments in the TCR a and~ chain loci allows for a large number
of distinct CDR3 sequences to be encoded. CDR3 sequence diversity is further increased by template-independent addition and deletion of nucleotides at the V 13-D13, D13-J13, and
V a-Ja junctions during the process of TCR gene rearrangement (Paragraph 45, lines 5-30). \
Regarding claims 246-248, Robins teaches that assay technology uses two pools of primers to provide for a highly multiplexed PCR reaction where the "forward" pool has a primer specific to each V segment in the gene (several primers targeting a highly conserved region are used, to simultaneously capture many V segments) and the "reverse" pool primers anneal to a conserved sequence in the joining ("J") segment (Paragraph 50, lines 1-5). Also, Robins teaches that the amplified segment pool includes adequate sequence to identify each J segment and also to allow for a J-segment-specific primer to anneal for resequencing and this enables direct observation of a large fraction of the somatic rearrangements present in an individual and this in tum enables rapid comparison of the TCR repertoire in individuals with an autoimmune disorder ( or other target disease indication) against the TCR repertoire of controls (Paragraph 50, lines 5-10). Therefore, Robins teaches that the adaptive immune system can in theory generate
an enormous diversity of T cell receptor CDR3 sequences far more than are likely to be expressed in any one individual at any one time (Paragraph 51, lines 1-3).
Robins teaches that the forward primers are modified at the 5' end with the universal forward primer sequence compatible with the Illumina GA2 cluster station solid-phase PCR and similarly, all of the reverse primers are modified with the GA2 universal
reverse primer sequence where the 3' end of each forward primer is anchored at position -43 in the V~ segment, relative to the recombination signal sequence (RSS), thereby providing a
unique V~ tag sequence within the amplified region (Paragraph 96, lines 1-5). Further Robins teaches that the thirteen reverse primers specific to each J~ segment are anchored in the 3' intron, with the 3' end of each primer crossing the intron/exon junction where thirteen sequencing primers complementary to the J~ segments were designed that are complementary to the amplified portion of the J~ segment, such that the first few bases of sequence generated will capture the unique J~ tag sequence (Paragraph 96).
However, Robins does not teach or suggest specific bait sets or probes that are specific to each portion of the targeted subgenomic interval.
Shojaei teaches the use of a sequence-specific DNA probe for hybridization-based capture of an immunoglobulin DH gene segment from a genomic DNA library (Abstract; Introduction: Paragraphs 2-3). Specifically, Shojaei teaches the development of a DH-specific DNA probe from a VDJ rearrangement and uses the probe to hybridize with and isolate genomic DNA containing DH gene sequences (Materials and Methods, 2.1 Development of DNA probe to putative bovine germline DH gene). Further, Shojaei teaches that the probe is specific for the DH gene sequence and was derived from a VDJ rearrangement, thereby teaching a probe configured to hybridize to a D segment (3.2: Short and long germline DH genes exist in bovine genome).
It would have been obvious to one of ordinary skill in the art at the time of the invention to modify the method of Robins to employ the sequence-specific hybridization probes taught by Shojaei for selective capture of the V, D, and/or J regions and rearranged V(D)J/VJ sequences analyzed by Robins. Shojaei teaches that a DNA probe can be designed from a VDJ rearrangement and used to specifically hybridize with and isolate a desired immunoglobulin gene segment from a nucleic acid library, thereby demonstrating the predictable use of sequence-specific probes to selectively capture immune-receptor sequences of interest.
Therefore one of ordinary skill in the art would therefore have been motivated to configure such probes according to the particular immune-receptor sequences targeted by Robins, including probes specific for individual V, D, or J segments, as well as probes spanning the VD, DJ, or VJ junctions or rearranged VDJ/VJ sequences, in order to selectively enrich the desired rearranged immune-receptor molecules before sequencing and thereby facilitate their detection and analysis. Robins specifically teaches V- and J-segment-specific oligonucleotides and sequencing of rearranged CDR3 sequences encompassing the V(D)J junction; where Robins specifically states that its reads generally capture the complete VNDNJ junction.
Applying Shojaei’s known sequence-specific hybridization approach to the different V(D)J/VJ targets disclosed by Robins would have constituted the predictable use of a known capture technique for its established purpose, selective hybridization to a nucleic acid sequence of interest, with a reasonable expectation of successfully enriching the corresponding immune-receptor sequences for subsequent sequencing and repertoire analysis. And, thus, one of ordinary skill in the art would have had a reasonable expectation of success in making this modification because Shojaei demonstrates that a DNA probe designed from a VDJ rearrangement successfully hybridizes to and permits isolation of the corresponding immunoglobulin gene sequence from a nucleic acid library. Thus, given the known sequences of V, D, and J segments and the rearranged VD, DJ, VJ, VDJ, and VJ junction sequences taught and analyzed by Robins, a skilled artisan would have reasonably expected that sequence-specific baits designed to those respective sequences, including baits spanning the respective junctions, would likewise specifically hybridize to and capture the corresponding target nucleic acids for subsequent sequencing and analysis.
Conclusions
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ELIZABETH ROSE LAFAVE whose telephone number is (703)756-4747. The examiner can normally be reached Compressed Bi-Week: M-F 7:30-4:30.
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, Heather Calamita can be reached on 571-272-2876. 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.
/ELIZABETH ROSE LAFAVE/Examiner, Art Unit 1684 /HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684
Prosecution Insights