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 .
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.
Claims 67-71, 77-87 are rejected under 35 U.S.C. 103 as being unpatentable over Kim et al. (US Pat. 7994098) in view of Manzo et al. (US PGPub 2024/0287505) and further in view of Hughes et al. (CSH Perspect Biol, 2017, 9(1)).
Regarding claim 67, Kim teaches a method for providing an array (DNA microarray – col. 3, lines 46-52 and 61-64) comprising first and second regions (col. 13, lines 9-14) on a substrate (substrate 100 – Fig. 1: below; col. 3, lines 61-64). Additionally, Kim teaches irradiating the substrate (124 and 126 – Fig. 13; col. 6, line 4) through a mask comprising an opening corresponding to a boundary region between the first and second regions (inverse mask pattern 112 – Fig. 1; col. 6, lines 28-38) thereby blocking (capped 130 – Fig. 14) nucleic acid molecules immobilized in the boundary region (col. 13, lines 47-49).
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Kim Figure 1
Furthermore, Kim teaches attaching first and second nucleotides to first and second nucleic acid molecules immobilized in the first and second regions, respectively (col. 13, lines 9-21). However, while Kim teaches conventional light directed DNA array synthesis (col. 13, lines 9-21), Kim does not teach attaching oligonucleotide molecules to nucleic acid molecules via ligation.
Manzo teaches a method (Fig. 5: annotated below; p. 2, para [0036]) for attaching oligonucleotide molecules (“second oligonucleotide” – p. 7, para [0116]) via ligation (abstract; p. 5-6, para [0103], lines 5-11) to generate extended nucleic acid molecules (“secondary indexed polynucleotide”).
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Manzo Figure 5, annotated
Additionally, there would be motivation before the effective filing date of the instant application to combine the oligo ligation method of Manzo with the inverse capping method of Kim due to the recognized difficulty of accurately synthesizing long nucleic acid molecules in situ via standard light direct DNA synthesis. As stated by Hughes et al., a challenge arises from sequential base-by-base addition of nucleotides in that the error rate of incorporating each additional nucleotide accumulates over the course of synthesis, limiting the length of oligos that can be synthesized with fidelity (p. 7-8). Additionally, Hughes teaches that synthetic oligos can be assembled together to create longer sequences (p. 8). Furthermore, one of ordinary skill in the art would have a reasonable expectation of success in combining the aforementioned methods because assembly of nucleic acid molecules by ligation is a well-developed technique and, per Manzo, is compatible with immobilized nucleic acids (p. 1, para [0007]; Fig. 5).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to apply the method from Manzo of attaching oligonucleotide molecules to nucleic acid molecules via ligation to generate extended nucleic acid molecules to the method of Kim with a reasonable expectation of success, based on the motivation taught by Hughes.
Regarding claim 68, Kim teaches that the boundary region comprises part of the first region and/or part of the second region (Fig. 21, annotated below).
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Kim Figure 21, annotated
Claims 69-71 are drawn to the dimensions of both the array features and the boundary region between them. The feature dimensions achieved on a microarray are a result of the resolution of the photolithographic apparatus used to pattern the array. While Kim does not disclose dimensions of features or a boundary region, Kim teaches that the optics system described can obtain a “resolution of dimensions as small as 0.5 microns” (col. 9, lines 5-7). This demonstrates that the dimensions of an average diameter between 2 μm and 20 μm for the first and second regions, as well as a length of 1 to 20 μm and a width of about 0.5 μm for the opening corresponding to the boundary region were achievable by the method of Kim.
Furthermore, changes in relative dimensions, such as the relative dimensions of features and a boundary region, have been determined to be obvious. MPEP § 2144.04 (IV)(A) states:
In Gardner v. TEC Syst., Inc., 725 F.2d 1338, 220 USPQ 777 (Fed. Cir. 1984), cert. denied, 469 U.S. 830, 225 USPQ 232 (1984), the Federal Circuit held that, where the only difference between the prior art and the claims was a recitation of relative dimensions of the claimed device and a device having the claimed relative dimensions would not perform differently than the prior art device, the claimed device was not patentably distinct from the prior art device.
As the claimed dimensions do not change the performance of the method – i.e. producing an array – one of ordinary skill in the art would recognize that the method of Kim is compatible with the dimensions of claims 69-71, rendering them obvious.
Regarding claim 77, Kim also teaches a positive photoresist is applied to the substrate (col. 9, lines 38-40) and upon irradiation through the mask, the positive photoresist is degraded to expose nucleic acid molecules in the boundary region (col. 9, lines 27-30), while nucleic acid molecules in the masked region(s) remain covered by the positive photoresist (col. 12, lines 40-42).
Regarding claim 78, Kim further teaches inactivating the exposed nucleic acid molecules (col. 12, lines 43-45).
Regarding claim 79, Kim further teaches that the exposed nucleic acid molecules are modified at the 3’ or 5’ end (col. 12, lines 45-54), rendering the exposed nucleic acid molecules unavailable for ligation (col. 12, lines 58-61).
Regarding claim 80, Manzo teaches modified 3’ends (p. 11, para [0114], lines 10-13) where the modification comprises 3’ ddC (p. 16, para [0180], lines 10-11).
Regarding claim 81, Kim also teaches that the attaching step of (a) and/or (b) comprises photolithography (col. 1, lines 39-61) using a photoresist (col. 1, lines 58-61) or a 5’ photolabile protective group (col. 1, lines 47-48; col. 13, lines 45-47).
Regarding claim 82, the limitations of claim 67, including those recited in 82(II), are discussed above. Additionally, Kim teaches irradiating a substrate comprising an unmasked first region and a masked second region (col. 13, lines 11-14), whereby a photoresist (col. 1, lines 58-61) in the first region is degraded (claim 9) to render the first nucleic acid molecules in the first region available for ligation (col. 13, lines 14-15), whereas the second nucleic acid molecules in the second region are protected by a photoresist in the second region from ligation (claim 9).
Regarding claim 83, the limitations of claim 67, including those recited in 83(IV), are discussed above. Additionally, Kim teaches irradiating a substrate comprising an unmasked second region and a masked first region, whereby a photoresist in the second region is degraded to render the second nucleic acid molecules in the second region available for ligation, whereas the first nucleic acid molecules in the first region are protected by a photoresist in the first region from ligation (col. 13, lines 20-22).
Regarding claim 84, the limitations of claim 82, including those recited in 84(A), are discussed above. Additionally, Manzo teaches a first splint (Figure 5 – annotated above; p. 2, para [0036]) and that the first oligonucleotide comprises a first barcode sequence (p. 7, para [0116], lines 14-15), wherein the first splint hybridizes to the first oligonucleotide and the first nucleic acid molecules in the first region to generate the first extended nucleic acid molecules (Figure 5; p. 2, para [0036]).
Regarding claim 85, the limitations of claim 83, including those recited in 85(D), are discussed above. Additionally, while Kim does not explicitly teach removal of a first photoresist and applying a second photoresist, it is well known to those of ordinary skill in the art that in situ oligonucleotide synthesis using photoresists requires exchange of the photoresist layers in order to irradiate different features on an array. As shown in Figure 4 of Pirrung (2002, cited in IDS of 11/20/2023), the final step of the fabrication cycle involves stripping the photoresist, which is then applied again at the beginning of the next synthesis cycle. Therefore, stripping of a first photoresist before application of a second photoresist is anticipated by the disclosure of using photoresists for oligonucleotide array synthesis by Kim.
Furthermore, Kim teaches parallel combinatorial DNA synthesis as discussed previously in regards to claim 83. Applying the method of Manzo to the synthesis method of Kim, as discussed in regards to claim 67, would thereby result in the steps enumerated in claim 83 additionally using a second splint and barcode, as taught by Manzo and as discussed in regards to claim 84.
Regarding claims 86 and 87, these claims are drawn to continue the method of claim 85 by repeating the steps detailed in claims 84 and 85 in a “Round 2”. Therefore, the additional limitations being set forth in these claims are the repeated steps of claims 84 and 85 being applied to the first and second extended nucleic acid molecules to produce first and second further extended nucleic acid molecules by use of first and second Round 2 oligonucleotides comprising first and second Round 2 barcode sequences. This concept is exemplified by Kim, which states “the process is then repeated, binding another base to a different set of locations” (col. 9, lines 33-35). Furthermore, Manzo additionally discloses the process of ligating a Round 2 oligonucleotide (“third oligonucleotide” – p.12, para [0155]) to an extended nucleic acid molecule (“secondary indexed polynucleotide” – p.12, para [0155]) to obtain a further extended nucleic acid molecule (“tertiary indexed polynucleotide” – p. 13, para [0155]). Taken with the repeated cycles disclosed by Kim, claims 86 and 87 are rendered obvious.
Claims 72-76 are rejected under 35 U.S.C. 103 as being unpatentable over Kim et al. (US Pat. 7994098), Manzo et al. (US PGPub 2024/0287505), and Hughes et al. (CSH Perspect Biol, 2017, 9(1)) as applied to claims 67-71 and 77-87 above, and further in view of Zebala et al. (US Pat. 6159681).
Regarding claim 72, Kim, Manzo, and Hughes teach blocking nucleic acid molecules in the boundary region as well as the method of synthesizing extended nucleic acids by ligation of oligonucleotides to nucleic acid molecules. However, Kim and Manzo do not teach that the nucleic acid molecule is synthesized into the extended nucleic acid molecule prior to being removed, blocked, or inactivated.
Zebala et al. (US Pat. 6159681) teaches removal of nucleic acid molecules (col. 33, lines 37-58) that have been previously synthesized (col. 21-22, lines 58-2). Furthermore, Zebala teaches that removal of nucleic acid molecules can be useful in instances where, “it is desirable to alter the exposed biologic material so as to inhibit detection of a substance of interest in such regions” (col. 33, lines 42-44). It is desirable to remove an extended nucleic acid molecule in a boundary region, as evidenced by Kim disclosing that the negative effects of light diffraction, scattering, and flair can be significantly reduced by inactivating nucleic acid molecules in a boundary region (col. 3, lines 46-60). Additionally, a first oligonucleotide molecule attached to a second nucleic acid molecule (and vice versa) is a product of light diffraction, scattering, and flare, which is precisely what is being referred to by Kim. According to the motivations provided by Zebala and Kim, it would therefore be desirable to apply the method Zebala to inactivate a first oligonucleotide molecule attached to a second nucleic acid molecule in a boundary region.
Additionally, Zebala confirms that the disclosed removal of extended nucleic acids is compatible with photolithography synthesis methods (col. 21, line 67) on arrays (col. 17, lines 17-18), so one of ordinary skill in the art would have a reasonable expectation of success in applying the method of Zebala to the method of Manzo and Kim.
Therefore, it would have been obvious to one of ordinary skill in the art before the filing date of the claimed invention to apply the method of inactivating an extended nucleic acid molecule from Zebala to the method of providing an array of Kim and Manzo, based on the motivation taught in Zebala and Kim.
Regarding claims 73 and 74, Zebala further discloses that the inactivation comprises irradiating a nucleic acid molecule with irradiation sufficient to cleave the nucleic acid molecule, as well as removing the cleaved nucleic acid molecule (col. 33, lines 37-58).
Regarding claim 75, cleavage via irradiation is discussed in regards to claim 73 above. Additionally, Kim teaches application of a positive photoresist to the substrate (col. 9, lines 38-40) and upon irradiation through the mask, the positive photoresist is degraded to expose nucleic acid molecules in the boundary region (col. 9, lines 27-30).
Regarding claim 76, as discussed above, Kim teaches the application of a positive photoresist but is silent on the use of a negative photoresist. However, Zebala teaches application of a negative photoresist to the substrate (col. 3, line 48) and upon irradiation through the mask, the negative photoresist is strengthened to render nucleic acid molecules in the boundary region inactive or inaccessible for ligation (col. 14, lines 55-59; lines 63-67).
The use of negative photoresists in the manufacture of biomolecule microarrays is well known, as evidenced by Zebala, which states, “It will be readily apparent to those skilled in the art that the photoresist may also be selected from a wide variety of negative photoresists” (col. 27, lines 38-40). Though the tone is opposite from the positive photoresist of Zebala, the basic function of the photoresist is unchanged: to differentially pattern accessibility of surface groups using irradiation. As negative photoresists are known in the art and their use in the manufacture of DNA microarrays has been well characterized, one of ordinary skill in the art before the effective filing date of the present application, could have substituted the positive photoresist of Kim with the negative photoresist of Zebala to arrive at the method described in claim 76 with predictable results.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 67, 69, and 77-83 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 33, 35, 42-45, and 50 of copending Application No. 18215296 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the reference application anticipates the enumerated claims of the instant application.
Regarding claim 67, the reference application teaches a method for providing an array comprising attaching a first oligonucleotide to a first nucleic acid molecule immobilized in a first region (claim 33), attaching a second oligonucleotide to a second nucleic acid molecule immobilized in a second region (claim 45), and irradiating the substrate through a mask comprising openings corresponding to a boundary region thereby removing or blocking nucleic acid molecules in the boundary region (claim 33).
Regarding claim 69, the reference application teaches that the spot regions are no more than 5 microns in diameter (claim 50).
Regarding claims 77-80, the reference application teaches a positive photoresist is applied to the substrate and is degraded upon irradiation to expose nucleic acid molecules in the boundary region (claim 33). It further teaches that the exposed nucleic acid molecules are inactivated (claim 33) by modification of the exposed 3’ end with a 3’ dideoxy group (claim 35).
Regarding claim 81, the reference application teaches that the attaching step comprises using a photoresist (claim 42), a photo-cleavable protective group (claim 44), or a photo-cleavable polymer (claim 44) that blocks ligation (claim 42/44).
Regarding claims 82-83, the reference application teaches irradiating the substrate comprising an unmasked first region and a masked second region whereby a photoresist in the first region is degraded (claim 43) to render the first nucleic acid molecules available for ligation (claim 33). Additionally, it teaches that this method can be performed in multiple cycles of irradiating different regions (claim 45).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 67 and 81 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 7, and 37 of copending Application No. 17565028 in view of Kim et al.
Regarding claim 67, the reference application discloses a method for providing an array comprising: attaching first oligonucleotide molecules to first nucleic acid molecules immobilized in the first region via ligation to generate first extended nucleic acid molecules (claim 1); attaching second oligonucleotide molecules to second nucleic acid molecules immobilized in the second region via ligation to generate second extended nucleic acid molecules (claim 7); and irradiating the substrate through a mask (claim 37).
As cited previously, Kim teaches a method for blocking nucleic acid molecules immobilized in the boundary region by irradiating the substrate through a mask. Kim also provides motivation for applying this method to light directed DNA synthesis by stating that it would prevent “unwanted DNA synthesis in the inactive areas… resulting in purer quality DNA” (abstract). As the reference application describes a method for light directed DNA synthesis, it would be obvious for a person of ordinary skill in the art to combine the method of the reference application with that of Kim with a reasonable expectation of success.
Regarding claim 81, the reference application further discloses that the attaching steps of the previous method comprise photolithography using a photo-cleavable protective group that blocks ligation (claim 1).
This is a provisional nonstatutory double patenting rejection.
Claims 67, 69, and 81-87 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 19, 43, 51-52, 60, and 66 of copending Application No. 17565047 in view of Kim et al.
Regarding claim 67, the reference application discloses a method for providing an array, comprising attaching first oligonucleotide molecules to first nucleic acid molecules immobilized in the first region via ligation to generate first extended nucleic acid molecules (claim 1), repeating this step in a second region with second oligonucleotide and nucleic acid molecules (claim 66), and irradiating the substrate through a mask to form a pattern of oligonucleotide molecules on the substrate (claim 19). This renders claim 67 obvious in conjunction with the method of Kim via the same reasoning as presented in item 11a above.
Regarding claim 69, the reference application further discloses that the features are no more than 10 microns in diameter (claim 60).
Regarding claims 81-83, the reference application further discloses that the attaching steps comprise photolithography using a photoresist that is degraded to render nucleic acid molecules available for ligation only where irradiated (claims 1 and 66).
Regarding claims 84-85, the reference application further discloses the use of splints (claim 43) and barcodes (claims 1 and 66).
Regarding claims 86-87, the reference application further discloses attaching additional barcodes to the extended nucleic acid molecules in repeated cycles (claims 51 and 52).
This is a provisional nonstatutory double patenting rejection.
Claims 67, and 81-86 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 108-109, and 119 of copending Application No. 18215299 in view of Kim et al.
Regarding claim 67, the reference application discloses a method for providing an array comprising: attaching first oligonucleotide molecules to first nucleic acid molecules immobilized in the first region via ligation to generate first extended nucleic acid molecules (claim 108); attaching second oligonucleotide molecules to second nucleic acid molecules immobilized in the second region via ligation to generate second extended nucleic acid molecules (claim 109); and irradiating the substrate through a mask (claim 108). This renders claim 67 obvious in conjunction with the method of Kim via the same reasoning as presented in item 11a above.
Regarding claim 81, the reference application teaches that the attaching step comprises photolithography using a photoresist that blocks ligation (claim 108).
Regarding claims 82-83, the reference application further discloses that the attaching step comprises irradiating a substrate comprising an unmasked first region and a masked second region whereby a photoresist in the first region is degraded to render the first nucleic acid molecules in the first region available for ligation, whereas the second nucleic acid molecules in the second region are protected by a photoresist from ligation (claim 108). It additionally discloses repeating this process where the second region is unmasked and the first region is masked (claim 109).
Regarding claims 84-85, the reference application further discloses that the first and second oligonucleotides comprise first and second barcode sequences, and the use of a first and second splint to hybridize the first and second oligonucleotide molecules and the first and second nucleic acid molecules (claims 108 and 109).
Regarding claim 86, the reference application further discloses repeating the irradiating and attachment steps by performing a Round 2 comprising a Round 2 barcode and Round 2 splint used to generate a further extended nucleic acid (claim 119).
This is a provisional nonstatutory double patenting rejection.
Claims 67 and 81-86 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 96, 98, 100, 104-106, and 111 of copending Application No. 18342906 in view of Kim et al.
Regarding claim 67, the reference application discloses a method for providing an array comprising: attaching first oligonucleotide molecules to first nucleic acid molecules immobilized in the first region via ligation to generate first extended nucleic acid molecules (claim 96); attaching second oligonucleotide molecules to second nucleic acid molecules immobilized in the second region via ligation to generate second extended nucleic acid molecules (claim 96); and irradiating the substrate through a mask (claim 100). This renders claim 67 obvious in conjunction with the method of Kim via the same reasoning as presented in item 11a above.
Regarding claim 81, the reference application teaches that the attaching step comprises photolithography using a photoresist that blocks ligation (claim 98).
Regarding claims 82-83, the reference application further discloses that the attaching step comprises irradiating a substrate comprising an unmasked first region and a masked second region whereby a photoresist in the first region is degraded to render the first nucleic acid molecules in the first region available for ligation, whereas the second nucleic acid molecules in the second region are protected by a photoresist from ligation (claim 98). It additionally discloses repeating this in a different region (claim 96).
Regarding claims 84-85, the reference application further discloses that the first and second oligonucleotides comprise first and second barcode sequences, and the use of a first and second splint to hybridize the first and second oligonucleotide molecules and the first and second nucleic acid molecules (claims 104-106).
Regarding claim 86, the reference application further discloses repeating the irradiating and attachment steps by performing a Round 2 comprising a Round 2 barcode and Round 2 splint used to generate a further extended nucleic acid (claim 111).
This is a provisional nonstatutory double patenting rejection.
Claims 67, 81-82, and 84 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 44-45, 47, and 55 of copending Application No. 18342948 in view of Kim et al.
Regarding claim 67, the reference application discloses a method for providing an array comprising: attaching first oligonucleotide molecules to first nucleic acid molecules immobilized in the first region via ligation to generate first extended nucleic acid molecules (claim 44); attaching second oligonucleotide molecules to second nucleic acid molecules immobilized in the second region via ligation to generate second extended nucleic acid molecules (claim 44); and irradiating the substrate through a mask (claim 44). This renders claim 67 obvious in conjunction with the method of Kim via the same reasoning as presented in item 11a above.
Regarding claim 81, the reference application teaches that the attaching step comprises photolithography using a photoresist that blocks ligation (claim 47).
Regarding claims 82, the reference application further discloses that the attaching step comprises irradiating a substrate comprising an unmasked first region and a masked second region whereby a photoresist in the first region is degraded to render the first nucleic acid molecules in the first region available for ligation, whereas the second nucleic acid molecules in the second region are protected by a photoresist from ligation (claim 48). It additionally discloses repeating this process where the second region is unmasked and the first region is masked (claim 47).
Regarding claims 84, the reference application further discloses that the first and second oligonucleotides comprise first and second barcode sequences, and the use of a first and second splint to hybridize the first and second oligonucleotide molecules and the first and second nucleic acid molecules (claims 45 and 46).
Claims 67, 69, and 81 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 88, 94, 97, and 105-106 of copending Application No. 18343108 in view of Kim et al.
Regarding claim 67, the reference application discloses a method for providing an array comprising: attaching first oligonucleotide molecules to first nucleic acid molecules immobilized in the first region via ligation (claim 97) to generate first extended nucleic acid molecules (claim 88); attaching second oligonucleotide molecules to second nucleic acid molecules immobilized in the second region via ligation to generate second extended nucleic acid molecules (claim 94); and irradiating the substrate through a mask (claim 88). This renders claim 67 obvious in conjunction with the method of Kim via the same reasoning as presented in item 11a above.
Regarding claim 69, the reference application discloses that the regions are between 1 and 5 microns in diameter (claim 106).
Regarding claim 81, the reference application teaches that the attaching step comprises photolithography using a photoresist that blocks ligation (claim 105).
Conclusion
No claims are allowed.
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/ALEXANDRA OLSON/Examiner, Art Unit 1684
/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684