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 .
The claims dated 10/7/2025 are under consideration.
The amendments and arguments presented in the papers filed 10/7/2025 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 5/7/2025 listed below have been reconsidered as indicated.
a) The objections of claims 1, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 and 28 are withdrawn in view of the amendments.
b) The rejections of claims 1-3 and 27-29 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, are withdrawn in view of the amendments to the claims.
c) The rejections of: claim(s) 29 under 35 U.S.C. 102(a)(1) as being anticipated by KaramiNejadRanjbar (On the Origin, Progression, and Evolution of Ovarian Cancer. Thesis submitted. 2018); and claim(s) 29 under 35 U.S.C. 102(a)(1) as being anticipated by Makarov (WO 2015/117040 A1), are withdrawn in view of the amendments to claim 29.
The Examiner’s responses to the Remarks regarding issues not listed above are detailed below in this Office action.
New and modified grounds of rejection necessitated by amendment are detailed below and this action is made FINAL.
Claim Interpretation
Claim 1 in step “vi” recites the following: “to provide data for determining any single nucleotide variants, determining chromosome structural variations, or determining phasing information in the genome of the single cell or cell-group”. The phrase is interpreted as describing an intended result of the act of “sequencing the indexed DNA library”. The phrase does not limit the scope or the manner in which the act of “sequencing” is carried out.
Claim 27 includes claim language that is “optional”. The claims include the element “the forward and reverse indexing primers further provide respective 5' and 3' sequencing adapters onto the indexed PCR products that are suitable for use in a sequencing reaction” that is optionally included within the method. Claim scope is not limited by claim language that makes optional but does not require steps to be performed. MPEP 2111.04.
Claim 28 includes claim language that is “optional”. The claims include the element “the forward and reverse indexing primers further provide respective 5' and 3' sequencing adapters onto the indexed PCR products that are suitable for use in a sequencing reaction” that is optionally included within the method. Claim scope is not limited by claim language that makes optional but does not require steps to be performed. MPEP 2111.04.
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 19, 20 and 23 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.
The following are new rejections necessitated by the amendments to the claims.
Regarding claim 19, the claim recites “substantially all indexed DNA library sequences” starting in line 7. It is unclear what is encompassed by “substantially” all versus “a fraction of the indexed DNA library sequences”. The scope of “substantially all” and “a fraction” overlap as both encompass a portion of sequences but not all of the sequences. It is unclear when a real SNV is observed versus a false positive SNV.
Regarding claim 20, the claim recites “substantially present in all” and “not substantially present in all”. It unclear what the boundaries of “substantially” all are. For example, is it at least 99% percent of all sequences but not 95% of all sequences? Is it at least 95% of all sequences but not 90% of all sequences?
Regarding claim 23, the claim recites “i.e. non-cancerous” twice within separate parentheticals. It is unclear if the language sets forth a required limitation regarding the “normal” cells.
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 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) 1-30 is/are rejected under 35 U.S.C. 103 as being unpatentable over KaramiNejadRanjbar (On the Origin, Progression, and Evolution of Ovarian Cancer. University of Oxford, 2018; previously cited) in view of Makarov (WO 2015/117040 A1; previously cited).
The following includes maintained and new rejections as necessitated by the amendments to the claims.
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Regarding claims 1, 6 and 29-30, KaramiNejadRanjbar teaches a method depicted in Figure 1.3 – Library preparation procedure for Long Fragment Read (LFR) sequencing, which is the basis for “DigiPico”. A copy of the Figure is reproduced below.
The figures highlights elements relevant to steps (ii) to (vi) and serve for the basis of DigiPico.
KaramiNejadRanjbar teaches providing a 384-well plate (p. 35) as relevant to step (i). One would recognize that a typical 384-well plate used in molecular biology is laid out in a grid of “rows” and “columns”.
KaramiNejadRanjbar teaches providing genomic DNA as a sub-haploid dilution of genomic DNA into wells of 384-well plate (p. 35). KaramiNejadRanjbar further teaches denaturing DNA, rendering it single-stranded, diluting it and adding it to a well for subsequent amplification (p. 46). These teachings are relevant to step (ii).
KaramiNejadRanjbar teaches the use of WGA (p. 35), which amplifies the number of copies of molecules in the well, as relevant to step (iii).
KaramiNejadRanjbar teaches fragmenting the amplified molecules using CoREF and ligating adapters to the fragments (p. 35). KaramiNejadRanjbar teaches the ligated adapters are a looped common adapter sequence (p. 40). This teachings are relevant to step (iv).
KaramiNejadRanjbar teaches indexing molecules with ligated adapters using PCR to add indices to the adapter ligated molecules (p. 40). This teachings are relevant to step (v).
KaramiNejadRanjbar teaches sequencing the indexed molecules (p. 35) as relevant to step (vi).
KaramiNejadRanjbar provides further details of how the molecules are indexed. KaramiNejadRanjbar teaches combining each of 16 different i5 index sequences with each of 24 different i7 index sequences and this results in 384 unique index combinations which is required for DigiPico sequencing. See p. 40. The ordinary artisan would recognize a standard 384-well plate is divided into 16 rows and 24 columns. Therefore, it would have been obvious to have one i5 index sequence assigned to each row of the plate and to have one 75 index sequence assigned to each column of the plate.
Regarding claim 2, KaramiNejadRanjbar teaches the DigiPico approach described above is applied to the cells from a tissue biopsy (p. 134). See also, p. 178.
Regarding claim 3, KaramiNejadRanjbar teaches the cells are from tumor samples as a form of cancerous cells, pre-cancerous cells or suspected cancerous cells (p. 178).
Regarding claim 4, KaramiNejadRanjbar teaches the analysis of genomic DNA from 10-20 human cells (p. 3).
Regarding claim 5, KaramiNejadRanjbar teaches distributing genomic DNA in a 384 well plate (p. 32), presumably across the rows and the columns.
Regarding claim 7, KaramiNejadRanjbar teaches adding EvaGreen to the WGA reaction (p. 53).
Regarding claim 8, KaramiNejadRanjbar teaches adding and ligating looped adapters to fragments (p. 40). KaramiNejadRanjbar teaches fragmenting the amplified molecules using CoREF and ligating adapters to the fragments (p. 35). KaramiNejadRanjbar teaches the ligated adapters are a looped common adapter sequence (p. 40). This teachings are relevant to step (iv).
Regarding claims 9 and 10, KaramiNejadRanjbar teaches fragmenting using enzymes in a CoREF within the wells of the WGA plate (p. 181).
Regarding claim 11, KaramiNejadRanjbar teaches fragmenting the DNA, end repairing and dA-tailing (p. 181-182).
Regarding claim 12, KaramiNejadRanjbar teaches a loop adapter as described above. A loop adapter is well-known to have a stem-loop structure.
Regarding claim 13, KaramiNejadRanjbar teaches the ends of the fragments are symmetrical as the same adapter is added to each end (Fig. 2.2).
Regarding claim 15, KaramiNejadRanjbar teaches Ci sequences are provided in the adapted-DNA fragments based on the 16 different i5 index sequences with each of 24 different i7 index sequences as noted above.
Regarding claim 17, KaramiNejadRanjbar teaches the P5/P7 primers are used (p. 41 and 51), which includes sequencing adapter sequences.
Regarding claim 18, KaramiNejadRanjbar teaches filtering the indexed library via size selection (p. 44 and 182).
Regarding claim 19, KaramiNejadRanjbar teaches calling SNVs based on sequence data (p. 97, 100 and 111, 113, 130).
Regarding claim 20, KaramiNejadRanjbar teaches analyzing complementary sequences to identify SNPs (p. 184), for example via paired end sequencing (p. 183).
Regarding claim 21, KaramiNejadRanjbar teaches using BAM files to carry out analyses of sequence data (p. 59, 62, 76 and 79), which would be carried out “in silico”.
Regarding claim 22, KaramiNejadRanjbar teaches the analyses are carried out using artificial neural networks (p. 107, 109, 110 and 119).
Regarding claim 23, KaramiNejadRanjbar teaches the comparison of tumor and normal pairs in terms of their sequencing data (p. 82).
Regarding claim 24, KaramiNejadRanjbar teaches assigning a probability to an identified SNV (p. 97 and 165).
Regarding claim 25, KaramiNejadRanjbar teaches the sequencing data is in a FastQ file (p. 183 and 184).
Regarding claim 26, KaramiNejadRanjbar teaches trimming sequencing reads to remove adaptor sequences (p. 184).
Regarding claims 27 and 28, KaramiNejadRanjbar teaches a method depicted in Figure 1.3 – Library preparation procedure for Long Fragment Read (LFR) sequencing, which is the basis for “Digipico”. A copy of the Figure is reproduced above. The figure highlights elements relevant to steps (ii) to (v) and serve for the basis of DigiPico.
KaramiNejadRanjbar teaches providing a 384-well plate (p. 35) as relevant to step (i). One would recognize that a typical 384-well plate used in molecular biology is laid out in a grid of “rows” and “columns”.
KaramiNejadRanjbar teaches providing genomic DNA as a sub-haploid dilution of genomic DNA into wells of a 384-well plate (p. 35). KaramiNejadRanjbar further teaches denaturing DNA, rendering it single-stranded, diluting it and adding it to a well for subsequent amplification (p. 46). These teachings are relevant to step (ii).
KaramiNejadRanjbar teaches the use of WGA (p. 35), which amplifies the number of copies of molecules in the well, as relevant to step (iii).
KaramiNejadRanjbar teaches fragmenting the amplified molecules using CoREF and ligating adapters to the fragments (p. 35). KaramiNejadRanjbar teaches the ligated adapters are a looped common adapter sequence (p. 40). This teachings are relevant to step (iv).
KaramiNejadRanjbar teaches indexing the molecules having ligated adapters using PCR to add indices to the adapter ligated molecules (p. 40). This teachings are relevant to step (v).
KaramiNejadRanjbar provides further details of how the molecules are indexed. KaramiNejadRanjbar teaches combining each of 16 different i5 index sequences with each of 24 different i7 index sequences and this results in 384 unique index combinations which is required for DigiPico sequencing. See p. 40. The ordinary artisan would recognize the at standard 384-well plate is divided into 16 rows and 24 columns. Therefore, it would have been obvious to have one i5 index sequence assigned to each row of the plate and to have one 75 index sequence assigned to each column of the plate.
While KaramiNejadRanjbar teaches the above methods, KaramiNejadRanjbar does not specifically teach one index is added via ligation and as second index is added via indexing PCR of claim 1 and 16.
However, Makarov teaches an alternative method to add dual indices to a nucleic acid molecule.
In Fig. 13A, Makarov teaches ligation of an adaptor P1n to a nucleic acid, where P1n includes an index T’n hybridized to Tn. Makarov teaches a PCR reaction using a set of primers including Am, A and P1 to add a second index tm to the nucleic acid. Makarov teaches creating 96 combinatorial barcode sequences using a set of 8 P1n molecules and 12 Am molecules (para. 80). The ordinary artisan would recognize the at standard 96-well plate is divided into 8 rows and 12 columns. It would have been obvious that one P1n molecule is assigned to each row of the plate and one Am molecule is assigned to each column of the plate.
Regarding claim 14, Makarov teaches cleavage of adaptors having a uracil base (para. 148).
It would have been prima facie obvious to the ordinary artisan at the time of filing that one would have tried and substituted the dual indexing method of KaramiNejadRanjbar with the dual indexing method of Makarov. The two methods are variants of one another and are functionally equivalent because both end up with a nucleic acid being dual indexed in a two-step process.
Response to the 103 rejections
The Remarks argue the KaramiNejadRanjbar thesis was submitted in 2018 but was not published online until 2/20/2019 and was later available in hardcopy on 7/2/2019, citing to Exhibit A (p. 14-15). The Remarks argue KaramiNejadRanjbar is not prior art because it was not published until 2/20/2019 based on Exhibit A (p. 15). The Remarks further argue the thesis is by MOHAMMAD KERAMI NEJAD RANJPAR, the named inventor of the present application and as the priority date of the present application is 9 December 2019, this is within the 12-month grace period for consideration of prior publications (p. 13-14 and 15).
The arguments have been fully considered are not persuasive. First, it is noted that the author of the cited dissertation is “Mohammad KaramiNejadRanjbar” (emphasis added by Examiner), while the inventor is Mohammad Kerami Nejad Ranjpar (emphasis added by Examiner). There is no indication that the different spellings, in particular of “Ranjbar” and Ranjpar”, are in fact referring to the same person.
No declaration is provided with the email in Exhibit A that indicates the email pertains to the KaramiNejadRanjbar thesis. The email does not include any reference to “KaramiNejadRanjbar” as an author of the thesis being discussed nor does it provide the title of the thesis being discussed. MPEP 716.01(c) makes clear that “[t]he arguments of counsel cannot take the place of evidence in the record” (In re Schulze, 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965)). Thus, counsel’s arguments about Exhibit A cannot take the place of evidence in the recording the information provided in the emails of Exhibit A. Thus, the information in Exhibit A is not persuasive. According to Library Hub Discover, the cited dissertation was published in 2018 as indicated in the following screen shot (https://discover.libraryhub.jisc.ac.uk/search?q=On%20the%20origin%2C%20progression%20and%20evolution%20of%20ovarian&rn=4):
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The SOLO webpage from Oxford Libraries Online also indicates the cited thesis was published in 2018 (https://solo.bodleian.ox.ac.uk/discovery/fulldisplay?docid=alma990216104920107026&context=L&vid=44OXF_INST:SOLO&lang=en&search_scope=MyInst_and_CI&adaptor=Local%20Search%20Engine&tab=Everything&query=any,contains,On%20the%20origin,%20progression,%20and%20evolution%20of%20ovarian%20cancer&offset=0):
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The Open Access Theses and Dissertations list the publication date as 2018:
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Semantic Scholar also lists the cited dissertation as being published in 2018 (https://www.semanticscholar.org/paper/On-the-origin%2C-progression%2C-and-evolution-of-cancer-Karaminejadranjbar/918228adac05999cd46ee2515e110a70278b5fed):
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Google Books also lists the publication date for the cited thesis as 2018 (https://books.google.com/books/about/On_the_Origin_Progression_and_Evolution.html?id=thHixgEACAAJ):
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A complete copy of the webpages have also been provided.
Conclusion
No claims allowed.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH G DAUNER whose telephone number is (571)270-3574. The examiner can normally be reached 7 am EST to 4:30 EST with second Fridays Off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached at 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JOSEPH G. DAUNER/Primary Examiner, Art Unit 1682