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 .
Information Disclosure Statement
The IDS received on November 22, 2023 is proper and is being considered by the Examiner.
Drawings
The drawings received on August 31, 2023 are acceptable.
Claim Rejections - 35 USC § 112
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 12 and 22 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.
Claim 12 is indefinite for reciting the phrase, “including the non-subclone peptide in the immunogenic composition” for the following reasons.
Claim 12 depends from claim 11. Claim 11 recites that an immunogenic composition comprises a subclone peptide that is in-part encoded by a cell RNA sequence from a tumor cell. Claim 12 is directed to generating a non-subclone peptide, but instead of formulating its own immunogenic composition, is “included” in the immunogenic composition of claim 10 that is formulated from a tumor cell.
Claim 22 is indefinite for the following reasons.” Claim 22 recites that a statistical different is determined by a test consisting of a Markush group of elements that recite various tests known in the art, followed by the member, “and combinations and hybrids thereof.” A Markush group must be made up of a closed and each recited element. While such a group can recite “combination thereof” as part of its members (as there exists a finite member of such elements), the member, “hybrids thereof” does not allow one to determine just exactly how many hybrids exist.
Removal is required.
Conclusion
Claims 1-3, 5, 6, 8, 9, 11, 14-16, 18, 19, 23, 26, and 28-30 allowable.
Claims 12 and 22 are rejected.
Claims are free of prior art. The prior does not teach nor is there a motivation to arrive at a method for classifying a cell of a first sample by producing sequence data comprising a first somatic variant (i.e., first allele) from bulk DNA of the first sample; producing sequence data comprising a second somatic variant (i.e., second allele) from bulk DNA of a second sample, followed by producing RNA sequence from a cell of the same first sample, and aligning each cell RNA sequence to the first and second bulk DNA sequences in order to classify the cell as a first, second, or unknown cell based on the RNA sequence alignment.
The instant invention improves upon the sequencing information provided in a bulk DNA sequencing such as WGS (Whole Genome Sequencing) or exome sequencing:
“Whole genome sequencing involves sequencing the full DNA of cells of a tissue of interest. A similar technique, exome sequencing, involves sequencing the full complement of exons in the cells of the tissue of interest. The two techniques may generically be referred to as WxS sequencing. WxS sequencing is performed on bulk tissue, meaning that the genomic or exomic information of all the cells in the tissue is pooled prior to sequencing. Accordingly, genomic or exomic variation between cells of the tissue cannot be resolved by WxS sequencing” (section [0002])
“As stated above, WxS sequencing cannot resolve variation between cells of a tissue. Because tumors contains a variety of cells, including cancer cells (which can further be members of divergent subclonal lineages), stromal cells, non-cancerous cells, and immune cells, WxS sequencing may fail to provide information that would be useful to the clinician attempting to treat the subject’s cancer (section [0004])
By first generating a bulk DNA sequencing information containing alleles from respective samples (i.e., first and second), and generating an aligning RNA sequences produced from single-cell of the first sample allows the determination of genetic variation that exists between cells of tissues such as a tumor:
Accordingly, it would be desirable to have increased resolution of genetic variation between cells of a tissue, such as between cells of a tumor (section [0005])
While the broadest claim does not limit the nature of the first and second samples, the invention finds particular use in characterizing cells of tumor samples:
“Also, though not every cell in a tumor sample is necessarily a tumor cell, a tumor sample will contain tumor cells. The tumor cells are expected to provide one or more somatic variants relatively to healthy, non-cancerous cells from nearby healthy tissue (section [0057])
“Accordingly, the methods can also comprise classifying each somatic variant between the tumor sample bulk DNA sequence and the healthy tissue sample bulk DNA sequence. Specifically, each somatic variant can be classified as a tumor allele if present in the tumor sample bulk DNA sequence or a normal allele if present in the healthy tissue sample bulk DNA sequence (section [0058])
Inquiries
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Young J. Kim whose telephone number is (571) 272-0785. The Examiner can best be reached from 7:30 a.m. to 4:00 p.m (M-F). The Examiner can also be reached via e-mail to Young.Kim@uspto.gov. However, the office cannot guarantee security through the e-mail system nor should official papers be transmitted through this route.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner's supervisor, Gary Benzion, can be reached at (571) 272-0782.
Papers related to this application may be submitted to Art Unit 1681 by facsimile transmission. The faxing of such papers must conform with the notice published in the Official Gazette, 1156 OG 61 (November 16, 1993) and 1157 OG 94 (December 28, 1993) (see 37 CFR 1.6(d)). NOTE: If applicant does submit a paper by FAX, the original copy should be retained by applicant or applicant’s representative. NO DUPLICATE COPIES SHOULD BE SUBMITTED, so as to avoid the processing of duplicate papers in the Office. All official documents must be sent to the Official Tech Center Fax number: (571) 273-8300. Any inquiry of a general nature or relating to the status of this application should be directed to the Group receptionist whose telephone number is (571) 272-1600.
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/YOUNG J KIM/Primary Examiner
Art Unit 1637 March 2, 2026
/YJK/