DETAILED ACTION
Notice of Pre-AIA or AIA Status and New Examiner
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. Please note that the examiner for this application has changed. Please address future correspondence to Robert T. Crow (Art Unit 1683) whose telephone number is (571) 272-1113.
Election/Restrictions and Status of the Claims
3. The previous Requirement for Species Election is withdrawn.
Claims 154-160, 162-168, and 174-180 are under prosecution.
Information Disclosure Statement
4. The Information Disclosure Statements filed 25 March 2024, 12 June 2024, 13 April 2026,and 13 July 2026 are acknowledged and have been considered.
It is noted that the listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Specification
5. The use of trade names or marks used in commerce (including but not necessarily limited to Cy5), has been noted in this application. Any trade names or marks should be accompanied by the generic terminology; furthermore, the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Drawings
6. Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by:
I. The appropriate fee set forth in 37 CFR 1.17(h);
II. One set of color drawings or color photographs, as appropriate, if submitted via EFS-Web or three sets of color drawings or color photographs, as appropriate, if not submitted via EFS-Web; and, unless already present,
III. An amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
7. A statement from Applicant that there is no intention to have color drawings will result in acceptance of the drawings; otherwise, the conditions set forth above must be met in order for the color drawings to be accepted.
Claim Interpretation
8. The claims are each drawn to a “kit.” The specification, however, does not define this term, and so it is being interpreted to encompass any collection of reagents that includes all of the elements of the claims. Any further interpretation of the word is considered an “intended use” and does not impart any further structural limitation of on the claimed subject matter.
Claim Rejections - 35 USC § 103
9. 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.
10. 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.
11. Claims 154-160 and 175-179 are rejected under 35 U.S.C. 103 as being unpatentable over Gunderson et al. (U.S. Patent Application Publication No. US 2004/0018491 A1, published 29 January 2004) and, as applied to claims 158-159, as evidenced by fluorofinder.com ( [retrieved on 2026-09-10]. Retrieved from the Internet: <URL: app.fluorofinder.com/dyes/19-cascade-blue-ex-max-396-nm-em-max-410-nm>).
Regarding claim 154, Gunderson et al. teach kits comprising a solid support (i.e., a substrate) having a population microspheres comprising capture probes distributed thereon (paragraph 0042). Gunderson et al. further teach the beads are derivatized with IBL/DBL pairs (paragraph 0521), wherein the bead comprises an IBL (i.e., identifier binding ligand) bound to the capture probe on the bead (paragraphs 0574 and 0577) and comprises a nucleic acids sequence (paragraphs 0578 and 0582). Gunderson et al further teach a plurality of IBLs (paragraph 0587), and that the DBL (i.e., decoder binding ligand) is attached to a bead that comprises a fluorescent moiety (i.e., label; paragraph 0581), that there is a plurality of DBLs (paragraph 0578), and that the substrate (i.e., solid support) is chemically functionalized for attachment of the microspheres (paragraph 0545). Thus, Gunderson et al. teach all of the claimed limitations.
Regarding claim 155, the kit of claim 154 is discussed above. Gunderson et al. teach the identifier sequence (i.e., IBL) is part of the capture probe on the bead, and the IBL is bound to the decoder bead (i.e., DBL; paragraphs 0577 and 0581); Thus, both beads are immobilized on the solid support.
Regarding claim 156, the kit of claim 154 is discussed above. Gunderson et al. teach the second beads (i.e., decoder binding ligand beads) comprise a fluorescent moiety (i.e., label; paragraph 0581) that is coupled (i.e., attached) to the bead (paragraph 0585); thus, the beads are functionalized for the coupling.
Regarding claim 157, the kit of claim 156 is discussed above. Gunderson et al. teach bead diameters of 0.5 microns (paragraph 0554).
In addition, it is noted that the courts have stated where the claimed ranges “overlap or lie inside the ranges disclosed by the prior art” and even when the claimed ranges and prior art ranges do not overlap but are close enough that one skilled in the art would have expected them to have similar properties, a prima facie case of obviousness exists (see In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976); In re Woodruff, 919 F.2d 1575, 16 USPQ2d 1934 (Fed. Cir. 1990); Titanium Metals Corp. of America v. Banner, 778 F2d 775. 227 USPQ 773 (Fed. Cir. 1985) (see MPEP 2144.05.01).
The courts have also found that “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.” In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955). See MPEP 2144.05 II.
Therefore, the claimed ranges merely represent an obvious variant and/or routine optimization of the values of the cited prior art.
Applicant is advised that 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, Applicant should not merely rely upon counsel’s arguments in place of evidence in the record.
Regarding claims 158-160, the kit of claim 156 is discussed above. Gunderson et al. teach the fluorescent moiety is Cascade Blue (paragraph 0108), which has an excitation at 396 nm and an emission at 410 nm (i.e., claims 158-159), and is substantially non-fluorescent under excitation wavelengths between 490 and 650 nm (i.e., claim 160), as evidenced by fluorofinder.com.
Regarding claim 175, the kit of claim 154 is discussed above. Gunderson et al. teach polymerase and chain terminating nucleotides (paragraph 0020), which can be used to perform sequencing by synthesis.
It is noted that the courts have held that “while features of an apparatus may be recited either structurally or functionally, claims directed to an apparatus must be distinguished from the prior art in terms of structure rather than function.” In re Schreiber, 128 F.3d 1473, 1477-78, 44 USPQ2d 1429, 1431-32 (Fed. Cir. 1997). In addition, “[A]pparatus claims cover what a device is, not what a device does.” Hewlett-Packard Co. v. Bausch & Lomb Inc., 909 F.2d 1464, 1469, 15 USPQ2d 1525, 1528 (Fed. Cir. 1990) (emphasis in original).
The courts have also held that when a claim recites using an old composition or structure and the “use” is directed to a result or property of that composition or structure, then the claim is anticipated (In re May, 574 F.2d 1082, 1090, 197 USPQ 601, 607 (CCPA 1978)). The phrase “for performing” clearly defines a use, and therefore fails to define additional structural elements of the claimed kit. Because the cited prior art teaches the structural elements of the claim, the claim is obvious. See MPEP § 2114 and 2112.02.
Applicant is again cautioned to avoid merely relying upon counsel' s arguments in place of evidence in the record.
Regarding claims 176-177, the kit of claim 154 is discussed above. Gunderson et al. teach the fluorescent moieties are dyes (i.e., claim 176), in the form of Cascade Blue (i.e., claim 177; paragraph 0108).
Regarding claim 178, the kit of claim 154 is discussed above. Gunderson et al. teach beads made of polystyrene (paragraph 0553), as well beads comprising amines (paragraph 0486).
Regarding claim 179, the kit of claim 154 is discussed above. Gunderson et al. teach the sample is a viral sample (paragraph 0091) and thus does not comprise a cell or tissue sample.
In addition, it would have been obvious to have a kit that does not comprise a sample of any kind, so that a user could add their own sample.
12. Claims 162-163 and 180 are rejected under 35 U.S.C. 103 as being unpatentable over Gunderson et al. (U.S. Patent Application Publication No. US 2004/0018491 A1, published 29 January 2004) as applied to claim 154 above, and further in combination with Shenderov et al. (U.S. Patent Application Publication No. US 2010/0130369 A1, published 27 May 2010).
Regarding claims 162 and 180, the kit of claim 154 is discussed above in Section 11.
Gunderson et al. also teach the kits (i.e., compositions) have the added advantage of allowing quantifying of nucleic acid reactions (Abstract). Thus, Gunderson et al. teach the known techniques discussed above.
While Gunderson et al. teach rolling circle amplification on the first plurality of (i.e., the immobilized IBL) beads; paragraphs 0013 and 0195 and Figure 7), Gunderson et al. do not teach the rolling circle amplification products comprise a plurality of copies of the identifier sequence.
However, Shenderov et al. teach compositions wherein bead surfaces are coupled to identifiable molecules (thereby analogous to the IBLs of Gunderson et al.), which are nucleic acid sequences, and wherein the identifiable molecules are amplified by rolling circle amplification (i.e., claim 162; paragraphs 0015 and 0029). Rolling circle produces concatemers as products (paragraph 0013 of Gunderson et al); thus, the first plurality of beads are coupled to the plurality of concatemers comprising the copies of the identifier sequence (i.e., claim 180). Shenderov et al. further teach the identifiable sequences are then detected with labeled complementary sequences (analogous to the DBLs of Gunderson et al.), which has the added advantage of allowing either sequential or parallel readout (paragraph 0017). Thus, Shenderov et al. teach the know techniques discussed above.
It is noted that the courts have stated:
even though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process. In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985). See MPEP§ 2113.
The limitations regarding “generation is solution outside a cell of tissue sample” are part of the process of making the kit rather than structural limitations of the kit. Because the cited prior art teaches the claimed structural elements, the claim is obvious.
Applicant is again cautioned to avoid merely relying upon counsel' s arguments in place of evidence in the record.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of the cited prior art to arrive at the instantly claimed kit with a reasonable expectation of success. The ordinary artisan would have been motivated to make the combination because said combination would have resulted in a kit having the added advantages of allowing quantifying of nucleic acid reactions as explicitly taught by Gunderson et al. (Abstract) and allowing either sequential or parallel readout as explicitly taught by Shenderov et al. (paragraph 0017). In addition, it would have been obvious to the ordinary artisan that the known techniques of the cited prior art could have been combined with predictable results because the known techniques of cited prior predictably result in kits useful for nucleic acid detection.
Regarding claim 163, the kit of claim 162 is discussed above. Shenderov et al. teach the use of multiple colors for detecting a plurality of labels (paragraph 0018), as well as microbeads for multiplex optical coding of biomolecules (paragraph 0037). Thus, it would have been obvious for the plurality of labeled decoder beads (i.e., DBLs of Gunderson et al.) to comprise a plurality of differently labeled decoder beads each colored differently for a specific identifier sequence. Because each rolling circle product comprises the same identifier sequence, each different rolling circle product comprises a plurality of one color of decoder bead, with a different color bead for different identifier sequence on different products (i.e., arising from different targets).
13. Claims 164-166 are rejected under 35 U.S.C. 103 as being unpatentable over Gunderson et al. (U.S. Patent Application Publication No. US 2004/0018491 A1, published 29 January 2004) and Shenderov et al. (U.S. Patent Application Publication No. US 2010/0130369 A1, published 27 May 2010) as applied to claim 163 above, and further in combination with Irizarry et al. (U.S. Patent Application Publication No. US 2010/0094795 A1, published 15 April 2010).
Regarding claim 164, the kit of claim 136 is discussed above Section 12.
While Gunderson et al. teach comparison to a reference gene (i.e., wild-type; paragraph 0293), none of the previously cited prior art discussed identifier sequences for the reference genes.
However, Irizarry et al. teach identifier sequences (i.e., barcodes; Abstract), wherein reference gene barcodes are included, and which have the added advantage of allowing comparison with the sample to identify tissue types (paragraph 0014). Thus, Irizarry et al. teach the known techniques discussed above.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Irizarry et al. with the previously cited prior art to arrive at the instantly claimed kit with a reasonable expectation of success. The ordinary artisan would have been motivated to make the combination because said combination would have resulted in a kit having the added advantage of allowing comparison with the sample to identify tissue types as explicitly taught by Irizarry et al. (paragraph 0014). In addition, it would have been obvious to the ordinary artisan that the known techniques of Irizarry et al. could have been combined with the previously cited prior art with predictable results because the known techniques of Irizarry et al. predictably result in useful controls for nucleic acid reactions.
Regarding claim 165, the kit of claim 164 is discussed above. Gunderson et al. each planar glass substrates (paragraph 0540).
In addition, the courts have found that changes in shape are obvious (In re Dailey, 357 F.2d 669, 149 USPQ 47 (CCPA 1966)). Thus, the planar substrate is alternatively an obvious variant of the glass substrate of the cited prior art. See MPEP 2144.04 IV B.
Applicant is again cautioned to avoid merely relying upon counsel' s arguments in place of evidence in the record.
Regarding claim 166, the kit of claim 165 is discussed above. Gunderson et al. teach the identifier sequence (i.e., IBL) is part of the capture probe on the bead, and the IBLs are bound to the decoder beads (i.e., DBL; paragraphs 0577 and 0581); Thus, both beads are immobilized on the solid support.
14. Claims 167-168 are rejected under 35 U.S.C. 103 as being unpatentable over Gunderson et al. (U.S. Patent Application Publication No. US 2004/0018491 A1, published 29 January 2004), Shenderov et al. (U.S. Patent Application Publication No. US 2010/0130369 A1, published 27 May 2010), and Irizarry et al. (U.S. Patent Application Publication No. US 2010/0094795 A1, published 15 April 2010) as applied to claim 166 above, and further in combination with Williams et al (U.S. Patent Application Publication No. US 2015/0086994 A1, published 26 March 2015).
Regarding claims 167-168, the kit of claim 165 is discussed above in Section 13.
While Gunderson et al. teach incorporated of amine derivatized nucleotides for attaching to a bead surface (i.e., claims 167-168; paragraphs 0520 and 0557), and while Shenderov et al. teach amine modifications for coupling to beads (i.e., claims 167-168’ paragraphs 0028-0029), none of the previously cited prior art teaches incorporation of the amine modified nucleotides into the RCPs (i.e., claim 167).
However, Williams et al. teach incorporation of amino modified nucleotides during rolling circle replication (paragraph 0030), which has the added advantage of allowing incorporation as specific positions along the amplified product (paragraph 0140). Thus, Williams et al. teach the known techniques discussed above.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Williams et al. with the previously cited prior art to arrive at the instantly claimed kit with a reasonable expectation of success. The ordinary artisan would have been motivated to make the combination because said combination would have resulted in a kit having the added advantage of allowing incorporation of the amines at specific positions in the RCPs as explicitly taught by Williams et al. (paragraph 0140). In addition, it would have been obvious to the ordinary artisan that the known techniques of Williams et al. could have been combined with the previously cited prior art with predictable results because the known techniques of Williams et al. predictably result in reliable insertion of the amine groups desired by Gunderson et al. and Shenderov et al.
15. Claim 174 is rejected under 35 U.S.C. 103 as being unpatentable over Gunderson et al. (U.S. Patent Application Publication No. US 2004/0018491 A1, published 29 January 2004) as applied to claim 154 above, and further in combination with Abate et al. (U.S. Patent Application Publication No. US 2018/0216160 A1, published 2 August 2018).
Regarding claim 174, the kit of claim 154 is discussed above in Section 11.
Gunderson et al. also teach the kits (i.e., compositions) have the added advantage of allowing quantifying of nucleic acid reactions (Abstract). Thus, Gunderson et al. teach the known techniques discussed above.
While Gunderson et al. teach rolling circle amplification on the first plurality of (i.e., the immobilized IBL) beads; paragraphs 0013 and 0195 and Figure 7), Gunderson et al. do not teach hydrogel beads.
However, Abate et al. teach rolling circle amplification (paragraph 0110) as well as hydrogel beads, and that hydrogel beads have the added advantage of permitting a large number of oligonucleotides to be synthesized on the bead (paragraph 0099). Thus, Abate et al. teach the known techniques discussed above.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of the cited prior art to arrive at the instantly claimed kit with a reasonable expectation of success. The ordinary artisan would have been motivated to make the combination because said combination would have resulted in a kit having the added advantages of allowing quantifying of nucleic acid reactions as explicitly taught by Gunderson et al. (Abstract) and permitting a large number of oligonucleotides to be synthesized on the beads as explicitly taught by Abate et al. (paragraph 0099). In addition, it would have been obvious to the ordinary artisan that the known techniques of the cited prior art could have been combined with predictable results because the known techniques
Conclusion
16. No claim is allowed.
17. Any inquiry concerning this communication or earlier communications from the examiner should be directed to Robert T. Crow whose telephone number is (571)272-1113. The examiner can normally be reached M-F 8:00-4:30.
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Robert T. Crow
Primary Examiner
Art Unit 1683
/Robert T. Crow/Primary Examiner, Art Unit 1683
Prosecution Insights