DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Objections
2. Claims 25-27 is objected to because of the following informalities: Each of these claims references the step (S4), this seems to be carried over from the original claim set filed 08 December 2022. All other specific references to the various steps seem to have been removed, and these should be removed as well for consistency. Appropriate correction is required.
Claim Rejections - 35 USC § 112
3. 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.
4. Claims 21-51 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
A. Claim 21 recites the phrase “contacting a sample comprising nucleic acid molecules of lymphocytes with M forward primers and N reverse primers, wherein M is an integer equal to or larger than one and N is an integer equal to or larger than one…” It is unclear based on the claim language how this limitation is intended to limit the claim; are M and N related to the absolute number of each primer molecule (i.e., a higher concentration of one primer vs another as in asymmetric PCR), do the M forward primers and N reverse primers account for the unique molecular identifier described in ¶ 7 of the claim (i.e., since the UMI is random does each UMI represent an ‘integer’ with respect to the M forward or N reverse primers such that the ratio of M:N relates to the length/diversity/presence of a UMI region on either the forward or reverse primer), or does each ‘integer’ of the M forward or N reverse primers differ by their target sequence (i.e., they relate to a set of multiplexed primers that amplify different regions of the nucleic acid molecules of lymphocytes). Additionally, the claim recites M forward primers and N reverse primers, and it is further unclear how this is coherent with the embodiment where M is an integer equal to one and N is an integer equal to one. For these reasons this claim lacks clarity and therefore it is indefinite.
B. Claims 22-51 are further rejected for being dependent on a previously rejected claim.
Claim Rejections - 35 USC § 103
5. 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.
6. Claims 21-46, 50, 51 are rejected under 35 U.S.C. 103 as being unpatentable over Godfrey et al (United States Patent Application No. US20180051277, published 22 February 2018) in view of Faham et al (United States Patent Application No. US20160355893, published 08 December 2016).
Regarding claim 1, Godfrey teaches an embodiment with M forward primers and N reverse primers, wherein either primer or each primer is a hairpin primer, and each hairpin primer comprises a random barcode/unique identifier sequence (UID; [0127] and [0065]). In this embodiment each forward hairpin primer with a different barcode represents one of the M forward primers (i.e., M is an integer greater than one) and each reverse hairpin primer with a different barcode represents one of the N reverse primers (i.e., N is an integer greater than one). Godfrey teaches that a hairpin barcode primer (i.e., each forward and reverse primer) comprises, in the 5' to 3' direction: a 5' stem sequence, an adapter sequence, a barcode/UID sequence (i.e., a UMI), a 3' stem sequence and a target specific sequence ([0127]). Godfrey teaches that the 5' stem sequence and the 3' stem sequence each comprise sequence complementary to each other and are configured to hybridize to each other under a closed annealing temperature and not hybridize to each other at an open annealing temperature ([0127]). Godfrey teaches amplifying nucleic acid molecules by performing a PCR pre-amplification in which the annealing temperature is less than or equal to the closed annealing temperature, under which conditions the hairpin barcode primers remain in a closed configuration ([0008] and [0126]). This pre-amplification inherently incorporates the sequence on the hairpin primers into the target nucleic acid, including the barcode sequence, to produce a plurality of barcoded PCR products. Godfrey teaches the further amplification of the pre-amplification target nucleic acids (i.e., contacting the barcoded PCR products) by adapter specific forward primers and adapter specific reverse primers ([0136] and [0150]). Godfrey teaches that a portion of the cycles of this amplification step have an annealing temperature greater than or equal to the open annealing temperature of the hairpin barcode primers ([0136] and [0150]).
Godfrey teaches sequencing these products and their barcodes ([0040], [0244] and [0247]) and demultiplexing sequencing reads based on the incorporated UIDs (UMIs; [0208]).
Godfrey does not teach a method of determining lymphocyte clonality, contacting a sample comprising nucleic acid molecules of lymphocytes with M forward primers and N reverse primers, that the target-specific sequences of each hairpin barcode forward primer and hairpin barcode reverse primer are complementary to a respective portion of a T-cell receptor (TCR) for B-cell receptor (BCR) clonotype, that the sequence reads of the method comprise the TCR or BCR sequences, mapping the demultiplexed sequence reads to respective TCR or BCR clonotypes based on nucleic acid sequences of the TCR or BCR sequences, and determining lymphocyte clonality for the sample based on the demultiplexed and mapped sequence reads.
However, Faham teaches a method of determining lymphocyte clonality ([0019] and [0040]) comprising contacting a sample comprising nucleic acid molecules of lymphocytes with forward and reverse primers ([0019]). Faham teaches that sequence tags are attached to substantially every clonotype in a sample by PCR primers by annealing the tags to the nucleic acid molecules from T-cells or B-cells (i.e., the target-specific sequence is complementary to a respective portion of a TCR or BCR; [0033], [0034] and [0039]). Faham teaches mapping the demultiplexed sequence reads to respective TCR or BCR clonotypes based on nucleic acid sequences of the TCR or BCR and determining lymphocyte clonality for the sample based on the demultiplexed and mapped sequence reads ([0040] and [0041]).
It would have been obvious to one having ordinary skill in the art to have replaced the generic “target nucleic acids” taught by Godfrey with the lymphocyte derived nucleic acids taught by Faham to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this substitution because Faham specifically teaches that sequence tags (i.e., the hairpin primers taught by Godfrey) provide advantages in the accurate sequencing for medical and diagnostic applications ([0004]) and that measuring clonotype profile is beneficial for the monitoring of minimal residual disease in patients. In addition, on having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the use of sequence tags to increase the performance of sequencing experiments.
Regarding claims 22-24, Godfrey teaches 2-5 cycles of preamplification to produce a plurality of preamplification target nucleic acids (i.e., barcoded PCR products; [0008]).
Regarding claims 25-27, Godfrey teaches amplifying the preamplification target nucleic acids (i.e., barcoded PCR products) with at least 10 PCR cycles ([0008]).
Regarding claim 28, Godfrey teaches that sequence reads are grouped in “super-families” by their UID (i.e., their UMI; [0208]).
Regarding claim 29, Godfrey teaches that sequences are grouped into families by start position and barcode ID (i.e., demultiplexed and divided into groups having the same TCR or BCR sequence), and that non-reference bases were reported if they composed 100% of the reads in a family with 10-20 reads or at least 90% of reads in a family with greater than 20 reads (i.e., a predefined number of mismatches allowed for nucleotide sequences of TCR or BCR sequences in the same group; [0245]).
Regarding claims 30 and 31, Faham teaches quantifying the number of input immune receptor molecules ([0060]). Faham does not specifically teach that the TCR or BCR clonotypes are quantified based on the demultiplexed and mapped sequence reads.
However, it would have been obvious to one of ordinary skill in the art to modify the generic quantitation taught by Faham with counting the number of unique sequence tags present in the sequencing reads because Faham specifically teaches that every nucleic acid encoding an IgH receives a distinct and unique sequence tag ([0037]). The ordinary artisan would recognize that the number of distinct and unique sequences tags would relate to the number (i.e., quantity) of clonotypes in the sample. Additionally, Faham teaches that errors in the sequence tags are not significant because the sequence tags associated with the clonotypes are so far apart in sequence that a huge number of base changes could be sustained without one sequence tag becoming close in sequence to another sequence tag ([0019] and [0037]). It would have been obvious to one having ordinary skill in the art to have used the sequence analysis methods taught by Faham to quantify the number of TCR or BCR clonotypes in the sample as Faham suggests in [0060] to arrive at the instantly claimed invention with a reasonable expectation of success.
Regarding claim 32, Godfrey teaches adding protease after the pre-amplification step to inactivate Taq DNA polymerase (i.e., degrading a polymerase) prior to the second round of PCR (i.e., amplifying the barcoded PCR products; [0243]).
Regarding claims 33-35, Godfrey teaches that the 3' stem sequence is 12-15 nucleotides.
Regarding claims 36 and 37, Godfrey teaches that at least two destabilizing nucleotides are added 3' of the barcode sequence and 5' of the 3' stem sequence (i.e., between the UMI and the 3' stem sequence; [0134]).
Regarding claims 38-40, Godfrey teaches that the barcode sequence (i.e., the UMI sequence) is a random sequence of 12 nucleotides (i.e., k = 12; [0132]).
Regarding claims 41 and 42, Godfrey teaches a second PCR that is used to generate PCR products with Illumina adapter primers (i.e., the adapter specific primers comprise sequences complementary to the M forward and N reverse primers; [0089]). Godfrey teaches that the adapter specific forward primer comprises from the 5' end to the 3' end the Illumina P5 sequence and a sequence complementary to the adapter sequence of the M forward primers (SEQ ID NO: 74), and that the adapter specific reverse primer comprises from the 5' to 3' end the P7 sequence and a sequence complementary to the adapter sequence of the N reverse primers (SEQ ID NO: 75).
Regarding claim 43, Godfrey teaches an embodiment wherein the hairpin adapters comprise a common adapter sequence and PCR amplification is accomplished with universal forward and reverse adapter specific primers ([0168]). It would have been obvious to one having ordinary skill in the art to have modified the common adapter sequence taught by Godfrey with different adapter sequence to arrive at the instantly claimed invention with a reasonable expectation of success, because the ordinary artisan would be able to immediately envision the opposite scenario wherein the hairpin primers do not comprise a common sequence since there are only two adapter configurations available. Additionally, the MPEP 2123(I) says that a reference may be relied upon for all that it would have reasonably suggested to one having ordinary skill in the art.
Regarding claims 44 and 45, Godfrey teaches a PCR No. 1 wherein hairpins are closed at 60 C, and PCR No. 2 wherein the hairpins are open at 70 C ([0084]).
Regarding claim 46, Godfrey teaches an embodiment with a forward hairpin primer with a UID and a non-hairpin reverse primer without a UID (FIG 3, New Strategy 1, and [0085]). In this embodiment N is one (no UID) and M is larger than 2 (N14 UID). The alternate embodiment wherein M is one and N is larger than two would have been obvious to one having ordinary skill in the art because the ordinary artisan would have immediately been able to envision it as one of only two orientations given the depiction of New Strategy 1 in FIG. 3. In addition, MPEP 2123(I) states that a reference may be relied upon for all that it would have reasonably suggested to one having ordinary skill in the art.
Regarding claims 50 and 51, Faham teaches a method of characterizing minimal residual disease in a patient (i.e., disease characterization) based on the characterization of clonotype profiles ([0007]). Faham teaches that minimal residual disease means the remaining cancer cells after treatment, used in connection with lymphomas and leukemias (i.e., hematological diseases; [0086]).
7. Claims 47-49 are rejected under 35 U.S.C. 103 as being unpatentable over Godfrey et al (United States Patent Application No. US20180051277, published 22 February 2018) in view of Faham et al (United States Patent Application No. US20160355893, published 08 December 2016) as applied to claim 21 above, and further in view of Asbury et al (United States Patent Application No. US20150259734, published 17 September 2015).
Regarding claims 47-49, the combination of Godfrey in view of Faham teaches M forward primers that are multiple different hairpin barcode primers as discussed fully above and incorporated here. Faham teaches that each somatically recombined nucleic acid molecule (i.e., the claimed TCR or BCR) is labeled with a unique sequence tag (i.e., there is at least one hairpin barcode forward primer per variable region of the TCR or BCR; [0010]).
The combination of Godfrey in view of Faham does not specifically teach that the forward primers are complementary to a respective variable region of the TCR or BCR, nor do they teach that the reverse primer comprises a target-specific sequence complementary to a respective joining region of the TCR or BCR.
However, Asbury teaches forward primers comprising sequence tags (i.e., barcodes) are specific for the V region sequences and reverse primers are specific for J region sequences (FIG. 1A and [0024]).
It would have been obvious to one having ordinary skill in the art to have modified the target specific regions taught by Godfrey in view of Faham to have targeted the variable region as taught by Asbury to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Asbury specifically teaches that in embodiments related to recombined nucleic acids encoding immune receptors, usually at least portions of a V, D, or J region are present between the two binding locations of the primers ([0025]). In addition, one having ordinary skill in the art would have recognized that the known techniques of the cited references could have been combined with predictable results because the known techniques of the cited references predictably result in the sequencing and analysis of recombinant nucleic acids by primers comprising sequence tags (i.e., barcodes).
Double Patenting
8. The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
9. Claims 21-27, 29-31, 33-40, 44, 45, 50 and 51 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 of U.S. Patent No. 10557134 in view of Faham et al (United States Patent Application No. US20160355893, published 08 December 2016).
Claim 8 of the issued patent teaches all the limitations of claim 21 except the limitations wherein the method is used to determine lymphocyte clonality, wherein a sample comprising nucleic acid molecules of lymphocytes is contacted with M forward and N reverse primers, wherein the hairpin barcode forward primer comprises a target-specific sequence complementary to a respective portion of a T-cell receptor, wherein the sequence reads comprise TCR or BCR sequences, wherein mapping the demultiplexed reads to respective TCR or BCR clonotypes is based on nucleic acid sequences of the TCR or BCR sequences, and determining lymphocyte clonality for the sample based on the demultiplexed and mapped sequence reads.
However, Faham teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have replaced the generic “target nucleic acids” taught by this issued patent with the lymphocyte derived nucleic acids taught by Faham to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this substitution because Faham specifically teaches that sequence tags (i.e., the hairpin primers taught by the issued patent) provide advantages in the accurate sequencing for medical and diagnostic applications ([0004]) and that measuring clonotype profile is beneficial for the monitoring of minimal residual disease in patients. In addition, on having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the use of sequence tags to increase the performance of sequencing experiments.
The limitations of claims 22-27, 33-40, 44 and 45 are taught in issued claims 1, 4-8, and 15 of the issued patent.
The limitations of claims 29-31, 50 and 51 are taught by Faham as discussed fully above and incorporated here.
10. Claims 28, 32, 41-43 and 46 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 of U.S. Patent No. 10557134 in view of Faham et al (United States Patent Application No. US20160355893, published 08 December 2016) as applied to claim 21 above and further in view of Godfrey et al (United States Patent Application No. US20180051277, published 22 February 2018).
Regarding claims 28, 32, 41-43 and 46, the method of claim 21 is discussed fully above and incorporated here. This issued patent in view of Faham does not teach the limitations of these claims.
However, Godfrey teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method taught by the issued patent in view of Faham with the teachings of Godfrey to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make these modifications because Godfrey specifically teaches analogous methods related to the practice of using, sequencing, and analyzing sequencing data related to the hairpin primers taught by the issued patents. In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in using hairpin primers for the preparation of sequencing libraries.
11. Claims 47-49 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 of U.S. Patent No. 10557134 in view of Faham et al (United States Patent Application No. US20160355893, published 08 December 2016) and Godfrey et al (United States Patent Application No. US20180051277, published 22 February 2018) and further in view of Asbury et al (United States Patent Application No. US20150259734, published 17 September 2015).
Regarding claims 47-49, the method of claim 21 is discussed fully above and incorporated here. These limitations are not taught in the issued patent in view of Faham and Godfrey.
However, Asbury teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the target specific regions taught by the issued patent in view of Faham and Godfrey to have targeted the variable region as taught by Asbury to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Asbury specifically teaches that in embodiments related to recombined nucleic acids encoding immune receptors, usually at least portions of a V, D, or J region are present between the two binding locations of the primers ([0025]). In addition, one having ordinary skill in the art would have recognized that the known techniques of the cited references could have been combined with predictable results because the known techniques of the cited references predictably result in the sequencing and analysis of recombinant nucleic acids by primers comprising sequence tags (i.e., barcodes).
Conclusion
12. No claims are allowed.
13. Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN ELLIS YOUNG whose telephone number is (703)756-5397. The examiner can normally be reached M-F 0730 - 1700.
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/BRIAN ELLIS YOUNG/Examiner, Art Unit 1684
/JULIET C SWITZER/Primary Examiner, Art Unit 1682