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 .
DETAILED ACTION
Claim 1 is currently pending in the instant application, filed March 20, 2023.
Therefore, claim 1 is are under consideration to which the following grounds of rejection are applicable.
Priority
The present application filed March 20, 2023 is a CON of US Patent Application 15055407, filed February 26, 2016, which claims the benefit of US Provisional Patent Application 62/194,075, filed July 17, 2015; US Provisional Patent Application 62/173,899, filed June 10, 2015; US Provisional Patent Application 62/160,976, filed May 13, 2015; US Provisional Patent Application 62/128,849, filed March 5, 2015; and US Provisional Patent Application 62/126,397, filed February 27, 2015.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on October 9, 2025 has been considered. An initialed copy of the IDS accompanies this Office Action.
Claim Objections/Rejections
Specification Objection
The disclosure is objected to because of the following informalities: the as-filed Specification, filed March 30, 2023 and July 19, 2023, do not include the current status of US Patent Application No. 15/055,407 (now abandoned).
Appropriate correction is required.
This disclosure is objected to because it contains an embedded hyperlink and/or other form of
Browser-executable code (e.g., as-filed Specification, paragraph [0234], line 17). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; it is noted that this can be achieved by amending the hyperlink(s) to remove the web-link and/or http:// recitations. See MPEP § 608.01.
Claim Rejections - 35 USC § 112(b)
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.
Claim 1 is rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 1 is indefinite for the recitation of the term “the sample” such as recited in claim 1, lines 2 and 4. There is insufficient antecedent basis for the term “the sample” in the claim.
Claim 1 is indefinite for the recitation of the term “a second oligonucleotide” such as recited in claim 1, line 5 because claim 1 does not recite a “first oligonucleotide” such that it is unclear how there can be a “second oligonucleotide,” and it is unclear whether a different component of claim 1 represents a “first oligonucleotide” and, thus, the metes and bounds of the claim cannot be determined.
Claim 1 is indefinite for the recitation of the term “the sequences” such as recited in claim 1, line 7. There is insufficient antecedent basis for the term “the sequences” in the claim.
Claim Rejections - 35 USC § 102
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 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.
Claim 1 is rejected under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Robins, Harlan (hereinafter “Robins”) (US Patent Application Publication No. 20140322716, published October 30, 2014; effective filing date June 15, 2012).
Regarding claim 1, Robins teaches compositions and methods are disclosed for uniquely tagging each rearranged gene segment that encodes a T cell receptor (TCR) and/or an immunoglobulin (Ig), in a DNA (or mRNA or cDNA reverse transcribed therefrom) sample from lymphoid cells, which permits accurate, high throughput quantification of distinct TCR and/or Ig encoding sequences; as well as, compositions and methods for quantitatively sequencing the genes that encode both chains of a TCR or Ig heterodimer in a single cell, for example, to characterize the degree of Tor B cell clonality in a sample (interpreted as mRNA encoding TCR alpha chain or beta chain; and a sample, claim 1) (Abstract). Robins teaches that several different strategies have been employed to sequence nucleic acids encoding adaptive immune receptors quantitatively at high throughput, and these strategies can be distinguished, for example, by the approach that is used to amplify the CDR3-encoding regions, and by the choice of sequencing genomic DNA (gDNA) or messenger RNA (mRNA) (interpreted a encompassing a first and second mRNA; and immunological analysis, claim 1) (paragraph [0011]). Robins teaches an oligonucleotide amplification primer composition comprising: (A) a first oligonucleotide amplification primer set comprising a plurality of forward oligonucleotide sequences of a general formula (A): U1-B1-V1, and a plurality of reverse oligonucleotide sequences of a general formula (B): U2-B2-J1, wherein U1 comprises an oligonucleotide sequence comprising a first universal adaptor oligonucleotide sequence, and U2 comprises an oligonucleotide sequence comprising a second universal adaptor oligonucleotide sequence; and/or B1 comprises an oligonucleotide that comprises either nothing or a first oligonucleotide barcode sequence of 6 to 20 contiguous nucleotides, and B2 comprises an oligonucleotide that comprises either nothing or a first oligonucleotide barcode sequence of 6 to 20 contiguous nucleotides, such that at least one of B1 or B2 is present; V1 comprises and oligonucleotide sequence comprising at least 15 and not more than 100 contiguous nucleotides of a V region encoding gene sequence of a first adaptive immune receptor, or the complement thereof; and J1 comprises an oligonucleotide sequence comprising at least 15 and not more than 80 contiguous nucleotides of (i) a joining (J) region encoding gene sequence of said first adaptive immune receptor, or the complement thereof, or (ii) a constant (C) region encoding gene sequence of said first adaptive immune receptor, or the complement thereof, and in each of the plurality of oligonucleotide sequences of general formula U1-B1-V1, V1 comprises a unique oligonucleotide sequence, and in each of the plurality of oligonucleotide sequences of general formula U2-B2-J1, wherein J1 comprises a unique oligonucleotide sequence (interpreting one or more oligonucleotide primers A and a first agent; and/or one or more oligonucleotide primers B as a second oligonucleotide; V1 and J1 are target-specific regions, each comprising a stochastic barcode region, claim 1) (paragraph [0019]). Robins teaches a method for labeling individual rearranged DNA sequences encoding first and second polypeptide sequences of an adaptive immune receptor heterodimer in a single lymphoid cell, comprising: contacting (A) a first plurality of individual microdroplets that each contain complementary DNA (cDNA) that has been reverse transcribed from messenger RNA (mRNA) of a single lymphoid cell, with (B) a second plurality of individual microdroplets, wherein the second plurality of individual microdroplets each contain (i) a first oligonucleotide amplification primer set that is capable of amplifying a first cDNA sequence encoding a first polypeptide of an adaptive immune receptor heterodimer, and (ii) a second oligo nucleotide amplification primer set that is capable of amplifying a second cDNA sequence encoding a second polypeptide of the adaptive immune receptor heterodimer, such that the first oligonucleotide amplification primer set comprises a composition of U1/2-B1-X1 described herein, and the second oligonucleotide amplification primer set comprises a composition of U3/4-B2-X2 described herein (interpreted as contacting mRNA encoding TCR chain with a first agent and first oligonucleotide comprising a target region and a stochastic region; and hybridizing first and second mRNA/cDNA, claim 1) (paragraph [0041]). Robins teaches that in a sample containing a plurality of sequence-diverse TCR or IG encoding gene segments, such as a sample comprising DNA (or mRNA transcribed therefrom or cDNA reverse-transcribed from such mRNA) from lymphoid cells in which DNA rearrangements have taken place to encode functional TCR and/or IG heterodimers (or in which non-functional TCR or IG pseudogenes have been involved in DNA rearrangements), a plurality of individual TCR or IG encoding sequences can each be uniquely tagged with a specific oligonucleotide barcode sequence as described herein, through a single round of nucleic acid amplification (e.g., polymerase chain reaction PCR), such that the population of tagged polynucleotides can then be amplified to obtain a library of tagged molecules, which can then be quantitatively sequenced by existing procedures such as those described, for example, in U.S. Ser. No. 13/217,126(US Pub. No. 2012/0058902), U.S. Ser. No. 12/794,507 (US Pub. No. 2010/0330571), WO/2010/151416, WO/2011/106738 (PCT/US2011/026373), WO2012/027503 (PCT/ US2011/049012), U.S. Ser. No. 61/550,311, and U.S. Ser. No. 61/569,118 (interpreting sequencing as identifying the sequences of the first mRNA and the second mRNA, claim 1) (paragraph [0074]). Robins teaches that Figure 1 shows a starting template population of genomic DNA or cDNA from a lymphoid cell-containing population, two or more cycles of PCR are performed using an oligonucleotide primer composition that contains primers having the general formula U1-B1-X as described herein, wherein the J-specific primer 110a contains a J primer sequence 100 that is complementary to a portion of the J segment, a barcode tag (BC1) 101, and also includes a first external universal adaptor sequence (U1) 102, while the V-specific primer 110b includes a V primer sequence 103 that is complementary to a portion of the V segment and a second external universal adaptor sequence (U2) 104 (interpreting oligonucleotide primers as a first agent and a second oligonucleotide comprising a target-specific region; and a stochastic region, claim 1) (paragraph [0076]). Figure 1 is shown below:
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Robins teaches that the second amplification primer set 120a, 120b can introduce sequencing platform-specific oligonucleotide sequences (Adap1, 105 and Adap2, 106 in Fig. 1), however these are not necessary in certain other related embodiments, wherein the second amplification primer set 120a, 120b can also optionally introduce a second oligonucleotide barcode identifier tag (BC2, 107 in Fig. 1), such as a single barcode sequence that can desirably identify all products of the amplification from a particular sample (e.g., as a source subject-identifying code) and ease multiplexing multiple samples to allow for higher throughput, such that the barcode (BC2, 107 in Fig. 1) is a modification that increases the throughput of the assay (e.g., allows samples to be multiplexed on the sequencer), but is not required (interpreting adap1 and adap2 as agents or oligonucleotides comprising a target-specific region and a stochastic region, claim 1) (paragraph [0079], lines 1-14).
Robins meets all the limitations of the claims and, therefore, anticipates the claimed invention.
Conclusion
Claim 1 is rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMY M BUNKER whose telephone number is (313) 446-4833. The examiner can normally be reached on Monday-Friday (6am-2:30pm).
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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.
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/AMY M BUNKER/Primary Examiner, Art Unit 1684