DETAILED ACTION
The present Office Action is responsive to the Amendment received on August 27, 2025.
Preliminary Remark
Claims 16-20 directed to a nonelected invention without traverse in the reply filed on April 30, 2025 are canceled.
Claims 21-24 are new.
Claim Rejections - 35 USC § 112
The rejection of claims 10-15 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter, made in the Office Action mailed on June 4, 2025 is withdrawn in view of the Amendment received on August 27, 2025.
Rejection – New Grounds, Necessitated by Amendment
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 21 and 23 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 21 and 23 recite the limitation, “wherein the molecule trap” is activated.
It is unclear whether “the” molecule trap is referring to “a molecule trap at an intersection” or one of the plurality of molecule traps.
Additionally, fusing a method of use with a parent product claim is indefinite.
The Federal Circuit decided an issue of first impression in that Court - whether a patent claim that covers both an apparatus and method of use of that apparatus passes muster under 35 USC §112, para. 2 (indefiniteness). Defending its "1-click system," Amazon won a summary judgment ruling of invalidity, IPXL Holdings, LLC v. Amazon.com, Inc., 333 F. Supp. 2d 513 (E.D. Va. 2004), which the Federal Circuit affirmed in part, 2005 U.S. App. LEXIS 25120.
After upholding the district court's claim constructions and affirming the finding that all but one of the asserted claims were anticipated, the Federal Circuit next affirmed the summary judgment of invalidity (for indefiniteness) for the remaining asserted claim, which read:
25. The system of claim 2 [including an input means] wherein the predicted transaction information comprises both a transaction type and transaction parameters associated with that transaction type, and the user uses the input means to either change the predicted transaction information or accept the displayed transaction type and transaction parameters. Claim 25 on its face is directed to a "system." However, it also recites use steps ("the user uses the input means to ...change the predicted transaction information ... ")
This claim was found indefinite by the district court.
Thus, for the above reasons, claims 21 and 23 are indefinite.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
The rejection of claims 1-7 and 10-15 under 35 U.S.C. 102(a)(1) as being anticipated by Duer et al. (US 2009/0312188 A1, published December 2009), made in the Office Action mailed on June 4, 2025 is maintained for the reasons of record.
Applicants’ arguments presented in the Amendment received on August 27, 2025 have been fully considered but they have not been found persuasive for the reasons discussed in the, “Response to Arguments” section.
The Rejection.
With regard to claim 10, Duer et al. teach the below device (see Figures 3F and 2A):
PNG
media_image1.png
504
651
media_image1.png
Greyscale
The device shown comprises:
PNG
media_image2.png
483
652
media_image2.png
Greyscale
a semiconductor chip having integrated therein (“substrate 304 includes multiple layers including Silicon layer …”, section [0088]): i) a plurality of wave guides (see below, excitation waveguides); ii) a plurality of nanochannels intersecting the plurality of waveguides (see microchannels 309 which is present together with the waveguide structure shown, “substrate 304 of the invention wherein substrate 304 additional includes reservoirs 311 and microchannels 309 in relation to the optical sensing sites 312 [or 212]”, section [0097]); iii) a molecule trap at an intersection of a waveguide and a nanochannel (“optical sensing sites 312 which can include etched wells to receive the sample”, section [0097]); and iv) photodetector operably connected to the molecular trap, the photodetector to detect a spectral signature from a molecule in the molecular trap (“detection of second light waves at each out-coupling waveguide is achieved using a detector that is a photodetector array”, section [0208]); and
a laser optically connected to the main waveguide (“system 100 … includes … an array of switchable lasers …”, section [0074]); and
computing system operably connected to the plurality of photodetectors to identify the spectral signature (“detected from a given collection waveguide 110 that results from sequencing-related dye activity at an optical sensing site 112”, section [0077]; “computer system … connected to an apparatus … for use with the scanning system … produce a result”, section [0238]).
With regard to claim 11, the system further comprises an immobilized DNA polymerase (“immobilizing a plurality of complexes comprising a template nucleic acid, a primer configured to hybridize to the template and a polymerase”, section [0013]; “polymerase in one embodiment is immobilized at the plurality of optical sensing sites”, section [0015]).
With regard to claim 12, the photodetector is proximate to the molecule trap (“the detector array can be a two-dimensional array including multiple elements arranged to receive the vertically dispersed light”, section [0075]).
With regard to claims 13 and 14, the light source can either be integrated on the same chip or alternatively external to the chip (see section [0131], “control of the switchable light source and detector array can either be integrated on the same chip as the light generator elements, detector elements, detector elements and waveguides or alternatively can be external to the chip”).
With regard to claim 15, the artisan also explicitly teaches that the light source can include light manipulating elements such as dispersive elements, filters, etc., section [0130]).
With regard to claim 1, the artisan also teach that a main waveguide can be branched into a plurality of waveguides (see Figure 5A, wherein each of the waveguide is branched into plurality of waveguides 521 to provide illumination to optical sensing sites 512 at the intersection regions 514; “excitation waveguides 508 include a plurality of branches 521 … for tapping light from the excitation waveguides and coupling it into the sensing wells”, section [0111]).
With regard to claim 2, the system further comprises a DNA polymerase in the molecule trap (“immobilizing a plurality of complexes comprising a template nucleic acid, a primer configured to hybridize to the template and a polymerase”, section [0013]; “polymerase in one embodiment is immobilized at the plurality of optical sensing sites”, section [0015]).
With regard to claim 3, the photodetectors are located proximate to the molecule traps (“the detector array can be a two-dimensional array including multiple elements arranged to receive the vertically dispersed light”, section [0075]).
With regard to claims 4 and 5, the light source can either be integrated on the same chip or alternatively external to the chip (see section [0131], “control of the switchable light source and detector array can either be integrated on the same chip as the light generator elements, detector elements, detector elements and waveguides or alternatively can be external to the chip”).
With regard to claim 6, the artisan also explicitly teaches that the light source can include light manipulating elements such as dispersive elements, filters, etc., section [0130]).
With regard to claim 7, the system further comprises a computing system operably connected to the plurality of photodetectors to identify the spectral signature (“detected from a given collection waveguide 110 that results from sequencing-related dye activity at an optical sensing site 112”, section [0077]; “computer system … connected to an apparatus … for use with the scanning system … produce a result”, section [0238]).
Therefore, Duer et al. anticipate the invention as claimed.
Response to Arguments:
Applicants traverse the rejection. Applicants’ arguments are addressed in the order in which they were presented.
Re: Laser:
Applicants contend that while Duer et al. teach a device having a “substrate 204, excitation waveguides 208 and collection waveguides 210, and sensing sites 212 … embodiment of FIG 2A does not have a laser, but does have a light source input 207”. Then Applicants state that while a different embodiment states that the system 100 of the embodiment of FIG 1 has a planar switchable light source 102 than [sic] can be an array of switchable lasers”, fails to complete their argument as to how this finding is not relevant to Applicants’ claims (page 9, Response).
The arguments are not found persuasive.
As to the reference made by the Office to the configuration of Fig 2A, this is to depict the configuration of the device disclosed by Duer et al., and while the Fig 2A does refer to the “light source” (102) as being directed to a switchable light source being “photo-cleaving light source” (see section [0083]), it is clear that this element is “switchable”, meaning that the artisans clearly contemplates this light source being a “laser,” as clearly shown in the description for the same “switchable light source” being a laser. This was clearly communicated in the Office Action:
“system 100 … includes … an array of switchable lasers …” (section [0074])
Therefore, this argument is simply not found persuasive.
The argument is therefore not persuasive.
Re: Photodetector array:
Applicants state that the cited section [0208] of Duer et al. provides a general discussion after the description of the numerous figures of Duer and does not point to a particular figure or embodiment and while paragraph [0208] does state that simultaneous detection of second light waves at each out-coupling waveguide is achieved using a detector that is photodetector array, pending claim 10 requires that the photodetector is operably connected to the molecular trap (page 9, Response).
Applicants contend that photodetector array of [0208] is not “specifically tied” molecule trap, but to the “out-coupling waveguide”, and not integrated into the chip (page 9, Response).
This argument has been carefully considered but has not been found persuasive.
Applicants’ attempt to tie a single alternative embodiment depicted in Fig. 2A for their argument while ignoring alternative embodiments which are suggested for the general configuration discussed by Duer et al. For example, Applicants chose to ignore the fact that Duer et al. explicitly teach that the light source is “switchable”, where the artisans clearly teach that one of such source is a “laser” with the Office Action explicitly pointing to the citation referencing this alternate embodiment.
Similarly, contrary to Applicants’ assertion, Duer et al. do teach photodetectors being proximate to the molecule trap as well as being integrated into the chip. This is clearly conveyed when reading the disclosure as a whole in context.
For example, Duer et al. teach that the waveguides are used to deliver a first light wave and the resulting second light waves are collected “simultaneously” using a detector that is a photodetector array:
“all in-coupling waveguides are provided with a first light wave and simultaneous detection of second light waves at each out-coupling waveguide is achieved using a detector that is a photodetector array” (section [0208])
“Excitation light can travel along the excitation waveguides 408 on the left hand side of the substrate 404 through, for example, chip-to-chip butt coupling. Excitation light can travel along the excitation waveguides 408 and couple into the optical sensing sites (e.g., wells) through an evanescent field tail … Excited fluorescence generated in the optical sensing site 412 can be collected along the long facet of the optical sensing site 412 into the funnels 417. The funnels 417 can channel the light into the collection waveguides 410. The light in the collection waveguides 410 can be coupled out at the ‘bottom’ of the substrate 404 into a detector array (not shown)” (section [0102])
This configuration is further illustrated below:
The device disclosed by Duer et al. is exemplified in Fig. 3B (see below):
PNG
media_image3.png
337
532
media_image3.png
Greyscale
As seen, the device has an optical sensing site located at intersecting regions and the intersection, and the device comprises a substrate (304).
This device from an exemplified top view (from Fig. 1A) also show that a photodetector array is functionally tied to receive the second light produced (i.e., excited fluorescence):
PNG
media_image4.png
524
639
media_image4.png
Greyscale
Duer et al. state:
“Detector array 106 … can include an array of elements 116. It is envisioned that any number of elements can be optically aligned with dispersive module 105 to receive light of desired wavelength … one embodiment … a set of four elements can be aligned with dispersive module 105 such that four different wavelengths of light (e.g., from four different fluorescent dyes) can be detected from a given collection waveguide 110 that results from sequencing-related dye activity at an optical sensing site 112” (section [0077])
Therefore, it is clear that the photo detector array is operably connected to the plurality of molecule traps (or optical sensing sties).
As to the photodetector array being located “proximate” to the plurality of molecule traps, Duer et al. state that “control of the switchable light source and detector array can either be integrated on the same chip as the light generator elements, detector elements and waveguides or alternatively can be external to the chip,” (section [0131]) which clearly imply the detector elements and waveguides are integrated on the chip and that their control, like them, can also be integrated on the same chip.
Therefore, contrary to Applicants assertion, Duer et al. teach that the detector element (detector array, see section [0129]) is located proximate and operably connected to the molecule traps (or optical sensing sites).
The argument is not found persuasive therefore.
Re: Microchannels:
Lastly, Applicants contend that the nanochannels are not taught in Fig. 2A, which again, as Office discussed above, are taking the teaching in piecemeal and not in their entirety. Duer et al. teach a configuration and discusses added features of their device. This is clear in their discussion pertaining to the microchannels which are configured to deliver the sample to the optical sensing sites:
“substrate 304 of the invention, wherein substrate 304 additionally includes reservoirs 311 and microchannel 309 in relation to optical sensing sites 312 (note that the waveguides are not shown in this illustration for easier viewing”… Microfluidics can be adapted to drive liquid (in this case the tested sample using the capillary effects across the substrate … this can be achieved by an arrangement of microchannels 309 … which force the sample from one or more reservoirs 311 to optical sensing sites 312 which can include etched wells to receive the sample” (section [0097])
Clearly, Duer et al.’s discussion is an embodiment which is added to the general depiction of the device exemplified in Fig. 2, not an entirely different configuration which does not have waveguides.
Therefore, Applicants’ arguments are not found persuasive and the rejection is maintained.
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 rejection of claims 8 and 9 under 35 U.S.C. 103 as being unpatentable over Duer et al. (US 2009/0312188 A1, published December 2009), made in the Office Action mailed on June 4, 2025 is maintained for the reasons of record.
In the Amendment received on August 7, 2025, Applicants rely solely on their arguments for the anticipation rejection over Duer et al. which have been responded to above as being unpersuasive. The present rejection is therefore maintained for the reasons already of record.
The Rejection.
The teachings of Duer et al. have already been discussed above.
While Duer et al. explicitly teach that their device is employed for the purpose of performing a DNA sequencing reaction, the artisans do not explicitly teach that a computer system is configured to identify the wavelength or fluorescence and correlate it to a molecule in the trap (or optical sensing site), or correlate to a nucleotide.
However, it would have been prima facie obvious to one of ordinary skill in the art would have been motivated to employ a computer algorithm to associate the signals arising from the optical sensing site to construct a nucleic acid sequence within the optical sensing site for the following reasons.
Duer et al. explicitly that that their device is designed for performing a DNA sequencing reaction with the below description:
“method includes the steps of (a) immobilizing a plurality of complexes comprising a template nucleic acid, a primer configured to hybridize to the template and a polymerase, at a plurality of optical sensing sites of a substrate, wherein the substrate is a part of a waveguide-based optical scanning system; (b) extending the primer by a single nucleotide with a polymerase and one or more fluorescent nucleotide analogues using a polymerase extension reaction … detecting the unique tag of the fluorescent nucleotide analog by optically scanning the substrate using the optical scanning system to identify the fluorescent nucleotide analogues incorporated by the polymerase reaction … recording the result of the optical scanning of the substrate … repeating steps …”, section [0175])
Given the maturity of the technology in nucleic acid sequencing reactions, one of ordinary skill in the art would have already recognized that detection of the incorporation events occurring at the optical sensing site and compilation of a nucleic acid sequence in the method of Duer et al. would have employed a computer system or would have been motivated to employ a computer system to perform the task as such have been a standard practice in the art, yielding no more than a predictable outcome.
In KSR, the Supreme Court particularly emphasized “the need for caution in granting a patent based on the combination of elements found in the prior art,” Id. at 415, 82 USPQ2d at 1395, and discussed circumstances in which a patent might be determined to be obvious. Importantly, the Supreme Court reaffirmed principles based on its precedent that “[t]he combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” Id. at 415-16, 82 USPQ2d at 1395. The Supreme Court stated that there are “[t]hree cases decided after Graham [that] illustrate this doctrine.” Id. at 416, 82 USPQ2d at 1395. (1) “In United States v. Adams, . . . [t]he Court recognized that when a patent claims a structure already known in the prior art that is altered by the mere substitution of one element for another known in the field, the combination must do more than yield a predictable result.”
Rejection – New Grounds, Necessitated by Amendment
Claims 21-24 are rejected under 35 U.S.C. 103 as being unpatentable over Duer et al. (US 2009/0312188 A1, published December 2009) in view of Rothberg et al. (WO 2016/023011 A1, published February 2016).
The teachings of Duer et al. have already been discussed above.
With regard to claims 21 and 23, the claims were rejected above for containing active steps for a product claim, but the Office construes the claims as having a characteristic of being capable of being “activated”. To this end, the Office contends that the molecular trap (or the optical sensing sites) “can” be activated by delivering of the reagents for sequencing (as suggested by Duer et al.).
With regard to claims 22 and 24, Duer et al. do not explicitly teach that the waveguides are tapers at the molecule trap.
Rothberg et al. teach a well-known means of adjusting the waveguides to focus the light through the sensor sites, that include the tapering measures:
“[w]aveguides 6-904 includes a pinched region where the cross-section width of waveguide 6-904 is smaller at a location proximate to the center of bullseye grating structure 6-910 … length of waveguides 6-904 that is tapered may be suitable amount to reduce excitation energy loss and/or improve coupling efficiency1” (page 80, line 30 to page 81, line 2)
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Duer et al. with the teachings of Rothberg et al., thereby arriving at the invention as claimed for the following reasons.
While Duer et al. did not explicitly teach that their optical sensing sites had a waveguide that was tapered at the connection, one of ordinary skill in the art would have recognized that the configuration of the waveguides would be subject to modifications so as to allow the excitation energy provided through the waveguides were appropriately sized in order to allow the optical sensing sites to properly excited. While Duer et al. did not explicitly teach that the optical sensing sites were of a dimension which required the waveguides to be tapered at their location of connection, doing so would have been well-within the purview of the ordinarily skilled artisan. As well, Applicants own specification does not disclose any reason for having the tapered configuration other than that which was expressed by Rothberg et al., that is, to reduce the energy loss at the site of connection.
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Inquiries
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Young J. Kim whose telephone number is (571) 272-0785. The Examiner can best be reached from 7:30 a.m. to 4:00 p.m (M-F). The Examiner can also be reached via e-mail to Young.Kim@uspto.gov. However, the office cannot guarantee security through the e-mail system nor should official papers be transmitted through this route.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner's supervisor, Gary Benzion, can be reached at (571) 272-0782.
Papers related to this application may be submitted to Art Unit 1681 by facsimile transmission. The faxing of such papers must conform with the notice published in the Official Gazette, 1156 OG 61 (November 16, 1993) and 1157 OG 94 (December 28, 1993) (see 37 CFR 1.6(d)). NOTE: If applicant does submit a paper by FAX, the original copy should be retained by applicant or applicant’s representative. NO DUPLICATE COPIES SHOULD BE SUBMITTED, so as to avoid the processing of duplicate papers in the Office. All official documents must be sent to the Official Tech Center Fax number: (571) 273-8300. Any inquiry of a general nature or relating to the status of this application should be directed to the Group receptionist whose telephone number is (571) 272-1600.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/YOUNG J KIM/Primary Examiner
Art Unit 1637 November 5, 2025
/YJK/
1 “Coupling of excitation energy to one or more sample wells of the integrated device” (page 71, lines 23-24)