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
Amendments
In the reply filed 05/27/2026, Applicant has amended claims 1, 8, 11-13, 16 and 54, and newly canceled claim 10.
Claim Status
Claims 1-9, 11-16 and 54-68 are pending and are considered on the merits. Claims 1 and 54 are independent claims.
Declaration under 37 CFR 1.132
The declaration under 37 CFR 1.132 filed by Dr. Morteza Roodgar on 05/27/2026 is insufficient to overcome the rejection of instant claims based upon 35 U.S.C 103 as set forth in the last Office action.
New Claim Objections
Claim 16 is objected to because of the following informalities:
Claim 16 recites “wherein the passaging the cells, further comprises passing the cells after about 12 hours to about 48 hours by placing each colony in the third container coated with the extracellular matrix comprises adding a serine/threonine kinase inhibitor to a medium in the third container”, which contains two predicators. It is recommended to change to “wherein the passaging the cells further comprises passing the cells after about 12 hours to about 48 hours by placing each colony in the third container coated with the extracellular matrix and comprises adding a serine/threonine kinase inhibitor to a medium in the third container”.
Appropriate correction is required.
Withdrawn Claim Rejections - 35 USC § 112(a)
The prior rejection of claims 1-16 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, for reciting new matter is withdrawn in light of Applicant’s cancellation of claim 10 and amendment to claim 1 to delete the subject matter directed to the second subset of PBMCs that does not undergo a progenitor-expansion step.
Withdrawn Claim Rejections - 35 USC § 112(b)
The prior rejection of claims 12-13 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, for insufficient antecedent basis is withdrawn in light of Applicant’s amendment to claim 1 to delete the second subset of cells.
Withdrawn Claim Rejections - 35 USC § 112(d)
The prior rejection of claims 8-9 under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form is withdrawn in light of Applicant’s amendment to claim 1 to delete the second subset of cells.
New Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 63 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 63 recites the limitation of “the plurality of feeder cells are mouse embryonic fibroblast (MEF) cells or SNL feeder cells”. However, the amended base claim 54 recites “the plurality of feeder cells are SNL feeder cells”. Thus, claim 63 fails to further limit the subject matter of the claim upon which it depends.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Withdrawn Claim Rejections - 35 USC § 103
The prior rejection of claims 1-9, 11-16 and 54-68 under 35 U.S.C. 103 as being unpatentable over Roodgar et al., (referred to as “GigaScience”. GigaScience, 9, 2020 July 10, p. 1-12. Prior art of record) as evidenced by Roodgar et al., (bioRxiv preprint. doi: https://doi.org/10.1101/635250; posted June 4, 2019. P. 1-22. Prior art of record) and in view of StemSpan (Information sheet of StemSpan Serum-Free Expansion Medium from StemCell Technologies. Published in 2018. P. 1-3), Rogers et al., (Nat Rev Genet. 2014;15(5):347-59. Prior art of record), Rim et al., (J. Vis. Exp. 2016; (118): e54650, p. 1-7), Jayakumar et al., (Scientific Data. 2021 June; 8: 159. P. 1-9. Prior art of record) and Madrid et al., (Current Protocols. 2021 March; 1, e88, p. 1-25) is withdrawn in light of Applicant’s amendment to claims 1 and 54 to recite new limitations of “the transcription factors are Klf2, Nanog, Tfcp2L1, and Stat3” and “the plurality of feeder cells are SNL feeder cells”.
New Claim Rejections - 35 USC § 112(a)
(Enablement)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-9, 11-16 and 54-68 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification does not reasonably provide enablement for a method for deriving iPSCs comprising transfecting cultured PBMCs with a combination of transcription factors being Klf2, Nanog, Tfcp2L1, and Stat3. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
The factors to be considered in determining whether undue experimentation is required are summarized In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988). The Court in Wands states: “Enablement is not precluded by the necessity for some 'experimentation.'” Clearly, enablement of a claimed invention cannot be predicated on the basis of quantity of experimentation required to make or use the invention. “Whether undue experimentation is needed is not a single simple factual determination, but rather is a conclusion reached by weighing many factual considerations.” (Wands, 8 USPQ2d 1404). The factors to be considered in determining whether undue experimentation is required include: (1) the quantity of experimentation necessary, (2) the amount or direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims. While all of these factors are considered, a sufficient amount for a prima facie case is discussed below.
The office has analyzed the specification in direct accordance to the factors outlined in In re Wands. MPEP 2164.04 states: "[W]hile the analysis and conclusion of a lack of enablement are based on factors discussed in MPEP 2164.01(a) and the evidence as whole, it is not necessary to discuss each factor in written enablement rejection." These factors will be analyzed, in turn, to demonstrate that one of ordinary skill in the art would have had to perform "undue experimentation" to make and/or use the invention and therefore, Applicant's claims are not enabled commensurate with the scope of the invention.
SCOPE OF THE INVENTION
Independent claim 1 and claim 54 encompass a genus of method for deriving iPSCs from a nonhuman primate comprising transfecting cultured PBMCs with a combination of transcription factors, wherein the transcription factors are Klf2, Nanog, Tfcp2L1, and Stat3.
It is noted the claimed method uses the transitional term “comprising”, and the wherein clause uses the predicator “are”, thus the claimed method is inclusive or open-ended and does not exclude additional, unrecited elements or method steps (see MPEP 2111.03). In other words, the claimed method encompasses transfecting a combination of transcription factors of Klf2, Nanog, Tfcp2L1 and Stat3, and any other appropriate transcription factors.
Regarding the combination of transcription factors, the instant specification recites, in the “Methods and Compositions” section (from p. 14), especially in the “Nonhuman Primate iPSC Generation” subsection (from p. 15), that “In some embodiments, transfecting includes transfecting with a combination of transcription factors so that the cells are induced to overexpress the transcription factors. For example, the transcription factors may include: c-myc, KLf4, Sox2, or Oct3/4. Additional or alternative transcription factors may be used and are within the scope of the present disclosure. For example, transcription factors such as Klf2, Nanog, Tfcp2L1 and Stat3 may additionally or alternatively be used” ([0097], also see [00109] and [00110]. Bolded by examiner). The one and only piece of experimental data shown in Figure 7 uses “the compositions and methods described above in the methods and compositions section and as shown in FIGs 3A-3B” ([00156], it is noted that FIGs 3A-3B show flow chart and schematic diagram of the method). Thus, the specification merely discloses the prophetic use of the transcription factors Klf2, Nanog, Tfcp2L1 and Stat3, but does NOT disclose any working example demonstrating the additional or alternative use of the transcription factors Klf2, Nanog, Tfcp2L1 and Stat3 to reprogram somatic cells into iPSCs.
Dependent claims 2-9, 11-16 and 55-68 encompass the expansion condition and further steps of generating an individualized genome assembly that matches with the iPSC. However, the specification does not disclose any method of reprogramming somatic cells into iPSCs by additionally or alternatively using the cited four transcription factors.
Therefore, the specification fails to describe the genus of method for deriving iPSCs from cultured PBMCs by additionally or alternatively using transcription factors of Klf2, Nanog, Tfcp2L1, and Stat3.
ACTUAL REDUCTION TO PRACTICE
As stated supra, the specification does not provide guidance for or a working example for a method for deriving iPSCs from cultured PBMCs by additionally or alternatively using transcription factors of Klf2, Nanog, Tfcp2L1, and Stat3. The absence of working examples necessitates further experimentation. In regard to the claimed genus of method, Applicant has only disclosed a conventional method for inducing iPSCs from somatic cells by using Oct3/4, Sox2, Klf4, and c-Myc (see [00154] and [00155]), but only disclosed a prophetic use of Klf2, Nanog, Tfcp2L1, and Stat3 (see above). Therefore, the specification does not provide sufficient guidance on how to make and use the claimed genus of method for deriving iPSCs from PBMCs by additionally or alternatively using transcription factors of Klf2, Nanog, Tfcp2L1, and Stat3.
STATE OF THE ART & QUANTITY OF EXPERIMENTATION
The method of using the claimed invention is not well established. Although reprogramming techniques are known, one of skill in the art would neither expect nor predict the production of iPSCs from cultured PBMCs according to the claimed genus of method.
To the extent that the specification only discloses a prophetic use of the transcription factors of Klf2, Nanog, Tfcp2L1 and Stat3 in reprogramming somatic cells, but fails to provide any factually supported objective evidence, the prior art is treated as enabling as the instant specification.
However, in regard to a method of reprogramming somatic cells into iPSCs by additionally or alternatively use of Klf2, Nanog, Tfcp2L1 and Stat3, prior art Martello et al., (Annu. Rev. Cell Dev. Biol. 2014. 30:647-75) summarizes the transcription factors used to derive iPSCs and teaches “The classic Yamanaka reprogramming cocktail is composed of three pluripotency factors, Oct4, Sox2, and Klf4, plus cMyc. Klf4 can be substituted by Klf2 or Esrrb, whereas the addition of other factors, such as Nanog, Tfcp2l1, and Sall4, is reported to increase reprogramming efficiency” (p. 660, para 1). Thus, the prior art only discloses some of the transcription factors Klf2, Nanog, Tfcp2L1 or Stat3 may be beneficial in reprogramming, but is silent on using a combination of Klf2, Nanog, Tfcp2L1 and Stat3 to reprogram somatic cells into iPSCs.
Therefore, to the extent of the disclosure from the instant specification and the prior art, the claimed method of using a combination of transcription factors of Klf2, Nanog, Tfcp2L1 and Stat3 to reprogram somatic cells, is highly unpredictable.
The physiological art is recognized as unpredictable (MPEP 2164.03). As set forth in In re Fisher, 166 USPQ 18 (CCPA 1970), compliance with 35 USC 112, first paragraph requires: “That scope of claims must bear a reasonable correlation to scope of enablement provided by specification to persons of ordinary skill in the art; in cases involving predictable factors, such as mechanical or electrical elements, a single embodiment provides broad enablement in the sense that, once imagined, other embodiments can be made without difficulty and their performance characteristics predicted by resort to known scientific laws; in cases involving unpredictable factors, such as most chemical reactions and physiological activity, scope of enablement varies inversely with degree of unpredictability of factors involved.” Moreover, the courts have also stated that reasonable correlation must exist between scope of exclusive right to patent application and scope of enablement set forth in the patent application (27 USPQ2d 1662 Ex parte Maize!.). In view of the foregoing, due to the lack of sufficient guidance provided by the specification regarding the issues set forth above, the state of the relevant art, and the breadth of the claims, it would have required undue experimentation for one skilled in the art to use the instant broadly claimed invention.
CONCLUSION
In conclusion, since the art teaches that the method for reprogramming somatic cells into iPSCs using a combination of transcription factors Klf2, Nanog, Tfcp2L1 and Stat3 is highly unpredictable, and the specification only discloses a prophetic use of such factors but does not provide ample guidance with respect to how to use the claimed method to derive iPSCs, one would be burdened with undue experimentation to use the claimed invention for deriving iPSCs by using a combination of transcription factors Klf2, Nanog, Tfcp2L1, and Stat3.
Applicant is invited to provide factually supported objective evidences to demonstrate the claimed method of transfecting with a combination of transcription factors Klf2, Nanog, Tfcp2L1 and Stat3, optionally with additional transcription factors, is both necessary and sufficient to reprogram somatic cells into iPSCs, so as to obviate this enablement rejection.
Examiner’s comment
To the extent that the specification only discloses a prophetic use of the transcription factors of Klf2, Nanog, Tfcp2L1 and Stat3 in reprogramming somatic cells, the prior art is treated as enabling as the instant specification. Since the prior art discloses some of the cited transcription factors may be beneficial in reprogramming, the combination of the transcription factors is “obvious to try” to reprogram somatic cells as discussed below for the sake of compact prosecution.
New Claim Rejections - 35 USC § 103
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.
Claims 1-8, 11-16, 54-59 and 63-68 are rejected under 35 U.S.C. 103 as being unpatentable over Roodgar et al., (referred to as “GigaScience”. GigaScience, 9, 2020 July 10, p. 1-12. Prior art of record) as evidenced by Roodgar et al., (bioRxiv preprint. doi: https://doi.org/10.1101/635250; posted June 4, 2019. P. 1-22. Prior art of record) and in view of StemSpan (Information sheet of StemSpan Serum-Free Expansion Medium from StemCell Technologies. Published in 2018. P. 1-3. Prior art of record), Martello et al., (Annu. Rev. Cell Dev. Biol. 2014. 30:647-75), Tang et al., (Stem Cells. 2012;30(12):2645-56), Pan et al., (J. Genet. Genomics. 2010;37:241-248) and Rogers et al., (Nat Rev Genet. 2014;15(5):347-59. Prior art of record).
With respect to independent claims 1 and 54, GigaScience teaches a method of chromosome-level genome assembly of a nonhuman primate, a pig-tailed macaque (abstract, related to dependent claim 7). To annotate the assembled genome, GigaScience teaches using RNAseq and proteomics data from the study animal’s PBMCs and iPSCs (generated from the PBMCs) (p. 9, left col, last para “Genome annotation”) and teaches “iPSCs were derived from PBMCs of the study animal [19]” (p. 8, left col, para “Study subject, sample preparation and DNA extraction”. Note that reference [19] is the reference of Roodgar (bioRxiv, 2019)), thus teaches a method for deriving iPSCs from nonhuman primate’s PBMCs using the method of Roodgar (bioRxiv, 2019).
In regard to the preamble and obtaining/recovering PBMCs steps of claims 1 and 54, Roodgar teaches a method for deriving induced pluripotent stem cells (iPSCs) from chimpanzees and a pig-tailed macaque (abstract and p. 11, last para). Roodgar teaches “blood samples were obtained from a 12-year old male pig-tailed macaque from the Johns Hopkins University colony. The PBMC (peripheral blood mononuclear cells) were isolated from whole blood in each sample” (p. 11, last para).
In regard to the step of dividing the obtained PBMCs into at least a first subset and a second subset in claim 54, as stated supra, GigaScience teaches the obtained PBMCs are used for extraction of high molecular weight (HMW) DNA and additionally iPSCs are derived from PBMCs of the study animal accordingly to the method of reference #19 (i.e., Roodgar) (see e.g., p. 8, left col, para “Study subject, sample preparation, and DNA extraction”). Thus, GigaScience teaches dividing the obtained PBMCs into at least a first subset (for deriving iPSCs) and a second subset (e.g., for extracting HMW DNA).
In regard to culturing the PBMCs in an HSPC expansion medium for a time period prior to transfection in claims 1 and 54, Roodgar teaches “PBMCs were cultured in medium to expand blood progenitor cells in StemSpan medium for 9 days” (p. 11, last para, note that the StemSpan medium is an HSPC expansion medium).
However, Roodgar is silent on the expansion medium comprising IL-3, IL-6, FLT-3, TPO and SCF in claim 1.
StemSpan teaches StemSpan serum-free expansion medium is used for the generation and culture of hematopoietic cell types, “in most applications, addition of specific hematopoietic growth factors, cytokines, and/or other compounds is required for optimal growth” (p. 1, “Product Description” para 2) and teaches to “add desired cytokines, growth factors, and other components to StemSpan SFEM” (p. 1, “Handling/Directions for Use”, step 2). StemSpan teaches the StemSpan expansion supplements are suitable for use with StemSpan expansion medium, such as StemSpan CD34+ Expansion Supplement (10X) (Catalog #02691) for culture and expansion of large numbers of human CD34+ progenitor cells, containing recombinant human (rh) SCF, rh TPO, rh IL-3, rh IL-6, and rh Flt3 ligand (p. 2, bullet point #1).
Therefore, it would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method for deriving iPSCs comprising culturing PBMCs to expand blood progenitor cells in HSPC expansion medium StemSpan disclosed by GigaScience as evidenced by Roodgar, by combining one or more of cytokines and growth factors including IL-3, IL-6, FLT-3, TPO and SCF as suggested by StemSpan with a reasonable expectation of success. Since GigaScience as evidenced by Roodgar intends to expand blood progenitor cells in StemSpan expansion medium (Roodgar, p. 11, last para), and since StemSpan suggests addition of specific hematopoietic growth factors and cytokines is required for optimal growth (p. 1, “Product Description” para 2, and see “Handling/Directions for Use”, step 2) and suggests a StemSpan CD34+ Expansion Supplement for culture and expansion of large numbers of human CD34+ progenitor cells containing recombinant human (rh) SCF, rh TPO, rh IL-3, rh IL-6, and rh Flt3 ligand (p. 2, bullet point #1), one of ordinary skill in the art would have had a reason to add an expansion supplement containing IL-3, IL-6, FLT-3, TPO and SCF to the StemSpan HSPC expansion medium as suggested by StemSpan in order to optimally expand blood progenitor cells for iPSC reprogramming.
In regard to transfecting the cultured PBMCs with a combination of transcription factors in claims 1 and 54, Roodgar teaches “the cells were transfected with Sendai virus of four transcription factors c-myc, KLf4, Sox2, Oct3/4 … on the day of reprogramming (day 0)” (p. 11, last para).
However, Roodgar is silent on the new limitation of the transcription factors being a combination of Klf2, Nanog, Tfcp2L1 and Stat3 in claims 1 and 54.
It is noted the claimed method uses the transitional term “comprising”, and the wherein clause uses the predicator “are”, thus the claimed method is inclusive or open-ended and does not exclude additional, unrecited elements or method steps (see MPEP 2111.03). In other words, the claimed method encompasses transfecting a combination of transcription factors of Klf2, Nanog, Tfcp2L1 and Stat3, and any other appropriate transcription factors, such as c-myc, KLf4, Sox2 or Oct3/4.
Prior art Martello summarizes the transcription factors used to derive iPSCs and teaches “The classic Yamanaka reprogramming cocktail is composed of three pluripotency factors, Oct4, Sox2, and Klf4, plus cMyc. Klf4 can be substituted by Klf2 or Esrrb, whereas the addition of other factors, such as Nanog, Tfcp2l1, and Sall4, is reported to increase reprogramming efficiency” (p. 660, para 1). Martello further teaches “LIF, MEKi, and GSK3i have all been shown to enhance reprogramming efficiency (…Tang et al. 2012)” (p. 659, last full para.) and “LIF stimulation leads to phosphorylation of the transcription factor Stat3” (p. 659, para 2). Tang, as referred to by Martello as “Tang et al. 2012”, teaches constitutively active Stat3 (Stat3C) transfection promotes the pluripotency establishment of MEFs during reprogramming (e.g., abstract, p. 2646, “Results”, subsection “Enhanced Stat3 Activation Promotes Direct MEF Reprogramming”). Thus, Martello and Tang teach that Klf2 can substitute Klf4, and that Nanog, Tfcp2l1 and active Stat3 can increase reprogramming efficiency.
Therefore, it would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method for deriving iPSCs comprising transfecting cultured PBMCs with a combination of transcription factors c-myc, KLf4, Sox2 and Oct3/4 disclosed by GigaScience as evidenced by Roodgar, by substituting Klf2 for Klf4 and combining Nanog, Tfcp2l1 and active Stat3 as suggested by Martello and Tang with a reasonable expectation of success. Since Martello and Tang teach that Klf2 can substitute Klf4, and teach Nanog, Tfcp2l1 and active Stat3 can increase reprogramming efficiency (see above), one of ordinary skill in the art would obviously have had a reason to try to use transcription factors Klf2, Nanog, Tfcp2L1 and Stat3 in place of Klf4 and in combination with c-myc, Sox2 and Oct3/4 in order to try to obtain increased reprogramming efficiency.
In regard to no more than one day post-transfection transferring the transfected cells into a container comprising a plurality of feeder cells, Roodgar teaches “on the day after transfection (day 1), all the cells transfected with Sendai virus were transferred into a 6-well plate (30,000 cells per well) each well containing ~150,000 mouse embryonic fibroblast (MEF) feeder cells” (p. 11, last para).
However, Roodgar is silent on the new limitation of the plurality of feeder cells being SNL feeder cells in claim 11 and claims 54 and 63.
Pan teaches SNL fibroblast feeder layers support derivation and maintenance of induced pluripotent stem cells (e.g., abstract). Pan teaches “investigators have generally used mouse embryonic fibroblasts (MEFs) as feeder cells. As proliferation of primary MEFs is limited, it is necessary to isolate MEFs from mouse fetuses repeatedly to supply feeders for ES cells or iPS cells culture. MEFs also tend to lose the capacity to support proliferation of ES cells or iPS cells with increasing passages” (p. 242, left col, para 1). Pan teaches the SNL feeder cell line is an immortalized cell line and has been manipulated to stably express LIF gene (p. 242, left col, para 2). Pan teaches the SNL feeder cell line has advantages over MEF cells because it can be easily maintained and expanded repeatedly over long periods (p. 247, left col, para 2).
Therefore, it would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method for deriving iPSCs comprising using MEFs feeder cells disclosed by GigaScience as evidenced by Roodgar, by substituting the MEF feeder cells with SNL feeder cells as suggested by Pan with a reasonable expectation of success. Since Pan teaches MEF cells have limited proliferation and tend to lose supportive capacity with increasing passages and teaches the SNL feeder cell line has advantages over MEF cells because it can be easily maintained and expanded repeatedly over long periods (see above), one of ordinary skill in the art would have had a reason to substitute with SNL feeder cells in order to take advantages of easy maintenance and repeated expansion over long periods to support derivation and maintenance of iPSCs as suggested by Pan.
In regard to no more than one day after transferring, transferring the cells to a second container in claims 1 and 54, Roodgar teaches “on day 2, the floating cells were transferred to new wells of 6-well plate” (p. 11, last para).
In regard to on selected days after transfer to the second container performing adding medium, changing medium and adding cell growth factors until a first cell colony appears in claims 1 and 54, Roodgar teaches “on day 3, 2mL of in Essential-6 media were added into existing 2mL StemSpan medium…. On day 5, all the medium in each well were removed and replaced by E6 medium. … On day 7, all medium was removed and 2 mL of E6 + 100 ng/mL of bFGF were added. On day 8, 9, and 10 media was changed and with E7 (E6 + 100ng/ul of FGF). From day 11, the media was replaced by E8 until days 16 to day 18 when the first colonies of iPSC were observed.” (p. 11, last para).
In regard to passaging the cells by placing each colony in a third container coated with ECM in claims 1 and 54, Roodgar teaches “each colony was manually picked with 1000μL pipet and were cultured on new matrigel-coated plates in E8 media and 2nM of TZV on the first day after passage” (p. 11, last para – p. 12, para 1).
In regard to expanding the first colony in claims 1 and 54, Roodgar teaches the iPSCs are washed and dissociated, and cultured in E8X medium with TZV on MEFs for each passaging during the expansion and maintenance (p. 12, para 1), thus teaches the first cell colonies are expanded. Roodgar teaches the iPSCs are differentiated into cardiomyocytes in vitro (p. 13, last para) and are injected to mouse in vivo for teratoma assay (p, 12, 2nd last para.).
However, GigaScience and Roodgar are silent on the nonhuman primate being a cynomolgus macaque in claims 1 and 54.
Nevertheless, GigaScience compares the phylogenetic relationships among the 3 macaque species (pig-tailed macaque, rhesus macaque and cynomolgus macaque) and human (see e.g., Fig 4). GigaScience acknowledges that different species of nonhuman primates exhibit varying levels of susceptibility to diseases. Studying the variation in disease susceptibility among primate species (including humans) necessitates reliable reference genomes that enable cross-species comparative genomics. However, the qualities of the genome assemblies and annotations for some of the Old World monkeys are inferior to that of the human genome [11] (see p. 2, “Introduction”, para 2). It is noted that the reference [11] is Rogers (2014).
Rogers, as referenced by GigaScience, teaches the two most commonly used nonhuman primates in biomedical research are the rhesus macaque and the cynomolgus macaque, and thus their importance as models for studies of human health and disease justifies extensive analysis of these genomes (e.g., p. 354, last para). Rogers teaches nonhuman primate genomics is expanding the scope of biomedical research with innovative analyses of primate models of human disease, but despite recent progress, both evolutionary and biomedical studies would benefit significantly from additional information (p. 357, right col, para 1). Rogers further teaches macaques generally have higher levels of intra-species genetic variation than humans (see e.g., p. 356, left col, para “Polymorphism within species and disease phenotypes”), which is assessed by individual primate genome projects (p. 349, last para).
Therefore, it would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of generating individualized genome assembly of a nonhuman primate pig-tailed macaque and annotating the assembly using data from the study animal’s iPSCs derived from PBMCs disclosed by GigaScience as evidenced by Roodgar, by substituting the pig-tailed macaque with a cynomolgus macaque as suggested by Rogers with a reasonable expectation of success. Since GigaScience compares the phylogenetic relationships among the 3 macaque species (pig-tailed macaque, rhesus macaque and cynomolgus macaque) and human (see e.g., Fig 4) and acknowledges the qualities of the genome assemblies and annotations for some of the Old World monkeys are inferior to that of the human genome (see p. 2, “Introduction”, para 2), and since Rogers teaches the cynomolgus macaque is one of the two most commonly used nonhuman primates in biomedical research that justifies extensive analysis of its genome (e.g., p. 354, last para), and teaches both evolutionary and biomedical studies would benefit significantly from additional information (p. 357, right col, para 1), one of ordinary skill in the art would have had a reason to substitute with a cynomolgus macaque as suggested by Rogers in the method of generating and annotating individualized genome assembly disclosed by GigaScience and Roodgar in order to perform extensive analysis on the genome of the cynomolgus macaque to benefit the biomedical studies of using cynomolgus macaques as a human disease model.
With respect to claims 2 and 55 directed to the expanding comprising washing with PBS and incubating with a cell detachment solution, claims 3 and 56 directed to the incubating occurring at about 37°C, and claims 4 and 57 directed to the expanding comprising aspirating and dissociating the iPSCs into a single cell suspension, Roodgar teaches “for subsequent passaging and expansion, the iPSCs were washed with PBS and were incubated using 1mL of Accumax for one well of a 6-well plate for 5 minutes at 37°C. The cells were then aspirated, and single cell dissociated” (p. 12, para 1, note that Accumax is a cell detachment solution).
With respect to claims 5 and 58 directed to differentiating the iPSCs into main lineages including mesoderm and claims 6 and 59 directed to differentiating the main lineages into final tissues, Roodgar teaches iPSCs are cultured and treated with CHIR99021 to induce mesodermal differentiation, and from day 7 onwards, cells are placed on RPMI+B27 supplemented with insulin until beating was observed (p. 13, last para “Differentiation of iPSC into cardiomyocytes” and see Supplementary Figure S3).
With respect to claim 7 directed to further comprising generating an individualized genome assembly of the at least one individual, as stated supra, GigaScience teaches a method of generating chromosome-level genome assembly of a NHP (e.g., abstract) and teaches annotating the assembled genome using RNAseq and proteomics data from the study animal’s PBMCs or iPSCs (generated from the PBMCs) (p. 9, left col, last para “Genome annotation”).
With respect to claim 8 directed to extracting HMW DNA from the PBMCs, this is examined as extracting HMW DNA from a subset of the PBMCs. As stated supra, GigaScience teaches a subset of PBMCs are used for the extraction of high molecular weight (HMW) DNA using the MagAtrract HMW DNA Kit. The average size of the extracted HMW DNA is ∼53 kb (Supplementary Fig. S1B) (p. 8, left col, para “Study subject, sample preparation and DNA extraction”). Thus, GigaScience teaches extracting HMW DNA from a subset of PBMCs by purification of archival quality DNA.
With respect to claims 12 and 64 directed to the step of transferring the transfected cells into the container having feeder cells further comprising adding a tankyrase 1/2 inhibitor in a range of about 1 µM to about 3 µM, as stated supra, Roodgar teaches all the cells transfected with Sendai virus are transferred into a 6-well plate containing mouse embryonic fibroblast (MEF) feeder cells to reprogram into iPSCs (p. 11, last para).
However, Roodgar is silent on adding a tankyrase 1/2 inhibitor in a range of about 1 µM to about 3 µM in this step in claims 12 and 64.
Nevertheless, Roodgar teaches optimizing nonhuman primate iPSC culture conditions by supplementing with 2μM XAV939 to inhibit Wnt/β-catenin canonical pathway and teaches XAV939 was critical for long-term maintenance of iPSC on MEFs (Figure 1A) (p. 3, last para). Roodgar further teaches the addition of XAV939 reduces spontaneous differentiation of iPSCs and helps maintain pluripotency in NHP iPSCs (p. 5, last para). It is noted that XAV939 is a tankyrase 1/2 inhibitor.
Therefore, it would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of transferring the transfected cells into a container having feeder cells to reprogram into NHP iPSCs suggested by GigaScience evidenced by Roodgar and in view of StemSpan, Martello, Tang, Pan and Rogers, by combining adding a tankyrase 1/2 inhibitor, e.g., XAV939 in a range of about 1 µM to about 3 µM as suggested by Roodgar with a reasonable expectation of success. Since Roodgar teaches supplementing with 2μM XAV939 results in long-term maintenance of NHP iPSC on MEFs and reduces spontaneous differentiation of iPSCs and maintains pluripotency in NHP iPSCs (p. 3, last para and p. 5, last para, see Fig 1A), one of ordinary skill in the art would have had a reason to add a tankyrase 1/2 inhibitor XAV939 of 1 µM to 3 µM as suggested by Roodgar in the step of transferring and reprogramming the transfected cells in order to reduce spontaneous differentiation and to maintain pluripotency of the derived iPSCs.
With respect to claims 13 and 65 directed to a ratio of the transfected cells to feeder cells being about 1:3 to about 1:7, as stated supra, Roodgar teaches on the day after transfection (day 1), all the cells transfected with Sendai virus were transferred into a 6-well plate (30,000 cells per well) each well containing ~150,000 feeder cells (p. 11, last para), thus teaches the ratio of the transfected cells to the feeder cells is about 1:3 to about 1:7 (30,000:150,000 = 1:5).
With respect to claims 14 and 66 directed to a Sendai virus vector, as stated supra, Roodgar teaches “the cells were transfected with Sendai virus of four transcription factors” (p. 11, last para).
With respect to claim 15 directed to a basic fibroblast growth factor (bFGF), and claim 67 directed to growth factors comprising a basic fibroblast growth factor (bFGF) and the iPSCs being cultured under feeder-free conditions using culture media and extracellular matrix substrates for maintenance of the iPSCs, as stated supra, Roodgar teaches “on day 7, all medium was removed and 2 mL of E6 + 100 ng/mL of bFGF were added” (p. 11, last para), thus teaches adding a basic fibroblast growth factor (bFGF) in claims 15 and 67. Roodgar teaches a step of maintaining iPSCs in an optimized feeder free condition comprising coating the wells with iMatrix-511 (i.e., an extracellular matrix substrate) in E8X medium (p. 11, para 2).
Accordingly, it would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to have chosen a feeder-free condition for maintenance of the iPSCs as taught by Roodgar with a reasonable expectation of success. Since Roodgar has reduced to practice a method of maintaining iPSCs in an optimized feeder free condition using culture media and extracellular matrix substrates (p. 11, para 2), one of ordinary skill in the art would have had a reason to choose this feeder-free condition to maintain the NHP iPSCs in order to reduce the immunogenic effect from xenogeneic feeder cells.
With respect to claim 16 directed to the new limitation of the passaging comprising passing the cells after about 12 hours to about 48 hours, and adding a serine/threonine kinase inhibitor to a medium in the third container, as stated supra, Roodgar teaches “each colony was manually picked with 1000μL pipet and were cultured on new matrigel-coated plates in E8 media and 2nM of TZV” (p. 11, last para – p. 12, para 1, it is noted that TZV is an inhibitor of Rho-associated coiled-coil containing protein kinase (ROCK) which is a serine/threonine kinase, thus TZV is a serine/threonine kinase inhibitor). In regard to passing the cells after 12 hours to about 48 hours, it would have been obvious for one ordinary skill in the art before the effective filing date of the claimed invention to have passed the cells after the claimed culture period because these steps are “routine optimization”. MPEP states “generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical” and “where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation”. See MPEP 2144.05(II)(A).
With respect to claim 68 directed to the passaging under feeder-free conditions and adding a serine/threonine kinase inhibitor, as stated supra, Roodgar teaches “each colony was manually picked with 1000μL pipet and were cultured on new matrigel-coated plates in E8 media and 2nM of TZV” (p. 11, last para – p. 12, para 1). It is noted that TZV is a serine/threonine kinase inhibitor. It is also noted that the cited step does not have feeder cells, thus the iPSC colonies are cultured under feeder-free conditions with a serine/threonine kinase inhibitor added to the medium.
Hence, the claimed invention as a whole was prima facie obvious to a person of ordinary skill before the effective filing date of the claimed invention in the absence of evidence to the contrary.
Response to Traversal:
Applicant’s arguments and Dr. Roodgar’s declaration filed on 05/27/2026 are acknowledged.
Applicant first argues that none of the references teach or suggest a cynomolgus macaque (Remarks, p. 11). Rogers (1) merely recognizes that cynomolgus macaques are important biomedical models and that genomic analysis of such species may be useful, but does not teach deriving iPSCs from PBMCs from cynomolgus macaques (Remarks, p. 12, para 2). Further, Rogers (2) expressly emphasizes that rhesus macaques and cynomolgus macaques are distinct species. Thus, Rogers teaches away from assuming that protocols optimized for pig-tailed macaques or rhesus macaques could simply be substituted into cynomolgus macaques with a reasonable expectation of success (Remarks, p. 12, para 3). Rogers (3) expressly identifies meaningful genomic and functional differences between cynomolgus and rhesus macaques, including differences in cytochrome p450 loci and drug metabolism pathways. Such disclosures would have cautioned one of ordinary skill in the art against assuming that PBMC-derived iPSC generation techniques optimized in one macaque species would necessarily function similarly in another species (Remarks, p. 13, para 2). Rogers (4) highlights additional species-specific genetic and immunological differences between macaque species. These disclosures further support that cynomolgus macaques are not simple substitutes for pig-tailed macaques or rhesus macaques in complex cellular reprogramming systems (Remarks, p. 13, para 3). Rogers teaches (5) differences in gene expression and amino acid sequences affecting pharmacokinetics that reinforces that one of ordinary skill in the art would not have possessed a reasonable expectation that protocols specifically developed for one macaque species could be directly transferred to another species without additional experimentation and optimization (Remarks, p. 13, last para – p. 14). (6) Dr. Roodgar declares that it would not have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of generating individualized genome assembly of a nonhuman primate pig-tailed macaque and annotating the assembly using data from the study animal's iPSCs from PBMCs suggested by GigaScience, Roodgar, and StemSpan, by substituting the pig-tailed macaque as suggested by Rogers with a reasonable expectation of success (Remarks, p. 14, para 2, and Declaration, para 4).
Applicant’s arguments and Dr. Roodgar’s declaration have been fully considered but they are not persuasive.
As a first matter, regarding Dr. Roodgar’s declaration (Remarks, p. 14, para 2, and Declaration, para 4), it is noted that Dr. Roodgar’s declaration does not refer to any factually supported objective evidence in the record to support the opinion, thus is insufficient to overcome the prior and instant rejection. Applicant is invited to provide factually supported objective evidence to support the declaration.
In response to argument that Rogers (1) merely recognizes that cynomolgus macaques are important biomedical models and that genomic analysis of such species may be useful, but does not teach deriving iPSCs from PBMCs from cynomolgus macaques (Remarks, p. 12, para 2). It is noted that prior art GigaScience evidenced by Roodgar has already taught the claimed method for deriving iPSCs from PBMCs from pig-tailed macaques. The difference between the claimed method and the method of GigaScience evidenced by Roodgar lies in that the claimed method uses the species of cynomolgus macaque. Since Rogers recognizes that cynomolgus macaques are important biomedical models and that genomic analysis of such species is useful, Rogers is cited to teach the motivation to apply the method of GigaScience evidenced by Roodgar to the species of cynomolgus macaque, as claimed in the instant claims. Furthermore, since GigaScience evidenced by Roodgar reduces to practice a method for deriving iPSCs from PBMCs of a NHP species of pig-tailed macaque, there would have been a reasonable expectation of success in applying the taught method to a related species of cynomolgus macaque to arrive at the claimed method (as further discussed below).
In response to arguments (2), (3), (4) and (5) above, the arguments are directed to Rogers’ teaching that rhesus macaques and cynomolgus macaques are distinct species evidenced by the differences in cytochrome p450 loci affecting pharmacokinetics and drug metabolism pathways, as well as additional species-specific genetic and immunological differences, such that one of ordinary skill in the art would not have possessed a reasonable expectation of success in applying the method to cynomolgus macaques. This is not found persuasive. Applicant is reminded that arguments of counsel cannot take the place of factually supported objective evidence in the record. See In re Schulze, 346 F.2d 500, 602, 145 USPQ 716, 718 (CCPA 1965), In re Huang, 100 F.3d 135, 139-40, 40 USPQ2d 1685, 1689 (Fed. Cir. 1996); In re De Blauwe, 736 F.2d 699, 705, 222 USPQ 191, 196 (Fed. Cir. 1984). In the instant case, the statement, that the differences in cytochrome p450 loci as well as additional species-specific immunological differences would result in lacking a reasonable expectation of success in applying the taught method to another species of NHP, is not supported by factually supported objective evidence in the record. Since Applicant does not provide any objective evidence demonstrating how the differences in, e.g., cytochrome p450, would affect the iPSC derivation, and since the taught method has been shown to successfully derive iPSCs from PBMCs from one species of pig-tailed macaque, and since prior art has demonstrated iPSCs can be derived from multiple cell types from multiple species (e.g., human and mouse), one of ordinary skill in the art would have had a reasonable expectation of success in applying the taught method to the claimed species of cynomolgus macaque.
Applicant further argues, and Dr. Roodgar declares that it would not have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method for deriving iPSCs comprising culturing PBMCs to expand blood progenitor cells in HSPC expansion medium STEMSpan disclosed by GigaScience as evidenced by Roodgar, by combining "interleukin-3 (IL-3), interleukin-6 (IL-6), fms-like tyrosine kinase 3 ligand (FLT-3), thrombopoietin (TPO), and stem cell factor (SCF)" with a reasonable expectation of success (Remarks, p. 14-15, and Declaration, para 3).
Applicant’s arguments and Dr. Roodgar’s declaration have been fully considered but they are not persuasive.
Similarly, as stated supra, it is noted that Dr. Roodgar’s declaration does not refer to any factually supported objective evidence in the record to support the opinion, thus is insufficient to overcome the prior and instant rejection. Applicant is invited to provide factually supported objective evidence to support the declaration.
Applicant further argues that the cited reference, especially the bioRxiv reference, fails to teach or suggest at least Klf2, Nanog, Tfcp2L1, and Stat3 as claimed transcription factors used for reprogramming (Remarks, p. 15-16).
Applicant’s arguments have been fully considered and they are persuasive. Therefore, the prior rejections have been withdrawn. However, as necessitated by amendment, new grounds of rejections have been made under 112(a) Enablement and 103 rejection in view of Martello and Tang, as stated supra.
Applicant further argues that the cited reference, especially the bioRxiv reference, fails to teach or suggest the new limitation the plurality of feeder cells are SNL feeder cells (Remarks, p. 16).
Applicant’s arguments have been fully considered and they are persuasive. Therefore, the prior rejections have been withdrawn. However, as necessitated by amendment, a new ground of rejection have been made under 103 rejection in view of Pan, as stated supra.
Applicant further argues that the cited reference, especially the bioRxiv reference, fails to teach or suggest passing the cells after about 12 hours to about 48 hours recited in claim 16. There is impermissible hindsight reconstruction. The bioRxiv reference provides no express teaching of this timing window and does not identify any overlap with the specifically claimed temporal range (Remarks, p. 16-17).
Applicant’s arguments have been fully considered but they are not persuasive.
One of ordinary skill in the art would have immediately expected that passing cells at a certain time interval, usually between 1-3 days depending on the growth rate and split ratio, is a routine and conventional technique in cell biology. Therefore, it would have been obvious for one ordinary skill in the art before the effective filing date of the claimed invention to have passed the cells after the claimed culture period because these steps are of “routine optimization”. MPEP states “generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical” and “where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation”. See MPEP 2144.05(II)(A). One of ordinary skill in the art would have performed routine optimization to result in the claimed temporal range, which is not from impermissible hindsight reconstruction.
Claims 9 and 60-62 are rejected under 35 U.S.C. 103 as being unpatentable over Roodgar et al., (referred to as “GigaScience”. GigaScience, 9, 2020 July 10, p. 1-12. Prior art of record) as evidenced by Roodgar et al., (bioRxiv preprint. doi: https://doi.org/10.1101/635250; posted June 4, 2019. P. 1-22. Prior art of record) and in view of StemSpan (Information sheet of StemSpan Serum-Free Expansion Medium from StemCell Technologies. Published in 2018. P. 1-3. Prior art of record), Martello et al., (Annu. Rev. Cell Dev. Biol. 2014. 30:647-75), Tang et al., (Stem Cells. 2012;30(12):2645-56), Pan et al., (J. Genet. Genomics. 2010;37:241-248) and Rogers et al., (Nat Rev Genet. 2014;15(5):347-59. Prior art of record), as applied to claims 1, 7-8, and 54 above, and further in view of Madrid et al., (Current Protocols. 2021 March; 1, e88, p. 1-25. Prior art of record) and Jayakumar et al., (Scientific Data. 2021 June; 8: 159. P. 1-9. Prior art of record).
With respect to claims 9 and 60-62, as stated supra, GigaScience teaches a method of generating chromosome-level genome assembly of a NHP (e.g., abstract) and teaches the study animal’s PBMCs are used to generate iPSCs (p. 9, left col, last para “Genome annotation”). GigaScience teaches a subset of PBMCs are used for the extraction of high molecular weight (HMW) DNA using the MagAtrract HMW DNA Kit. The average size of the extracted HMW DNA is ∼53 kb (Supplementary Fig. S1B) (p. 8, left col, para “Study subject, sample preparation and DNA extraction”). GigaScience teaches preparing two different genomic libraries (a linked-read library and a HiC library), sequencing the libraries on Illumina HiSeq 4000, and assembling and scaffolding the data to generate an genome assembly (p. 8, left col, last para – right col). GigaScience further teaches annotating the genome using RNAseq and proteomics data from the study animal’s PBMCs and iPSCs (generated from the PBMCs) (p. 9, left col, last para “Genome annotation”). Thus, GigaScience teaches the method further comprises generating an individualized genome assembly of the at least one individual wherein the genome assembly is matched to an iPSC line derived from the at least one individual such that a genomic sequence of the iPSC line corresponds to the individualized genome assembly of the at least one individual in claim 60, the method further comprises extracting HMW DNA from the second subset of PBMCs by purification of archival quality DNA in claim 61, and the method further comprises preparing a genome library from the HMW DNA, sequencing fragments of the HMW DNA in the library, and assembling and annotating the fragments to recreate the genome of the individual from which the PBMCs were obtained in claims 9 and 62.
However, GigaScience evidenced by Roodgar and in view of StemSpan, Martello, Tang, Pan and Rogers, are silent on a step of administering the iPSC line autologously in one translational in vivo validation study conducted in the same individual from which the iPSC line was derived in claim 60.
Nevertheless, Rogers teaches nonhuman primates are used as models for human diseases in the scope of biomedical research (p. 357, right col, para 1).
Madrid summarizes progress toward clinical translation of autologous iPSC-based cell therapies (see e.g., Table 1 in p. 4-5 for clinical trials and preclinical stages of development). Madrid teaches autologous iPSC-based cell therapies have promising outcomes and advantages such as a cell therapy product that can engraft without the risk of immune rejection, eliminating the need for immunosuppression and the associated side effects, and enabling autologous iPSC-based therapies to become a more commonplace treatment modality for patients (e.g., abstract).
Therefore, it would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method for deriving iPSCs from a non-human primate used as a model for human diseases in biomedical research as suggested by GigaScience evidenced by Roodgar and in view of StemSpan, Martello, Tang, Pan and Rogers, by combining a step of administering the iPSC line autologously in a translational in vivo validation study as suggested by Madrid with a reasonable expectation of success. Since Rogers teaches nonhuman primates are used as models for human diseases in the scope of biomedical research (p. 357, right col, para 1), and since Madrid teaches autologous iPSC-based cell therapies have promising outcomes in preclinical and clinical trials and have advantages such as a cell therapy product that can engraft without the risk of immune rejection (e.g., abstract), one of ordinary skill in the art would have had a reason to use the non-human primate as a model for human diseases and to administer the iPSC line autologously to the same study animal in a preclinical translational in vivo validation study as suggested by Rogers and Madrid in order to make progress toward clinical translation of autologous iPSC-based cell therapies to take advantage of the promising outcomes and reduced risk of immune rejection.
In regard to the long-read fragments in claims 9 and 62, as argued by Applicant, the term “long-read” is examined as being exemplified as being at least about 10,000 base pairs but may also be between about 5,000 base pairs to about 50,000 base pairs disclosed in specification [00122].
However, GigaScience evidenced by Roodgar and in view of StemSpan, Martello, Tang, Pan and Rogers, are silent on long-read fragments that are about 10,000 base pairs in claims 9 and 62.
Nevertheless, Rogers teaches improved assemblies with longer contigs and more complete coverage in high-quality sequence data (that is, comprehensive delineation of segmental duplications, and fewer genes with gaps and errors) are needed and new technologies that provide longer reads will yield better assemblies by filling remaining gaps. The Pacific Biosciences RS II platform is one plausible option for upgrading the quality of primate genomes (Ref# 105) (see p. 356, right col, para 2. It is noted that reference #105 is titled “Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology”).
Jayakumar teaches generating a genome assembly of nonhuman primate by sequencing and assembling long reads using Pacific Biosciences (referred to by Rogers) with a read N50 length of 12.05 kbp (i.e., about 12,050 base pairs. See abstract, p. 2, para “Sample preparation, sequencing, and de novo assembly”, also see Fig 1a). Thus, Jayakumar teaches a method of sequencing long-read fragments (N50 length of 12.05 kbp) to assemble a genome of NHP, related to claims 9 and 62.
Therefore, it would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of generating a genome assembly of a cynomolgus macaque by sequencing DNA fragments disclosed by GigaScience evidenced by Roodgar and in view of StemSpan, Martello, Tang, Pan and Rogers, by substituting the DNA fragments with long-read fragments suggested by Rogers and taught by Jayakumar with a reasonable expectation of success. Since Rogers suggests new technologies, e.g., the Pacific Biosciences RS II platform, that provide longer reads will yield better assemblies by filling remaining gaps for upgrading the quality of primate genomes (see p. 356, right col, para 2), and since Jayakumar teaches single-molecule long-read sequencing has drastically increased the contiguity of assemblies (p. 2, para 2) and teaches the resulted genome assemblies have high fidelity and outperform all the available assemblies of this species in terms of contiguity and are valuable resources for non-human primate models and provide an important baseline in human biomedical research (abstract), one of ordinary skill in the art would have had a reason to make this substitution in order to generate a genome assembly with high fidelity and increased contiguity to be used as a resource for non-human primate models and as an important baseline in human biomedical research (Jayakumar, abstract).
Hence, the claimed invention as a whole was prima facie obvious to a person of ordinary skill before the effective filing date of the claimed invention in the absence of evidence to the contrary.
Response to Traversal:
Applicant’s arguments and Dr. Roodgar’s declaration filed on 05/27/2026 are acknowledged and have been discussed above.
Conclusion
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 extension fee 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 date of this final action.
No claims are allowed.
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/JIANJIAN ZHU/Examiner, Art Unit 1631
/JAMES D SCHULTZ/Supervisory Patent Examiner, Art Unit 1631
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