DETAILED ACTION
The present Office Action is responsive to the Amendment received on November 14, 2025.
Preliminary Remark
Claims 2-7, 11, 12, 15, 18, 22, 23, 26-31, and 33 are canceled.
Claim Rejections - 35 USC § 112
The new matter rejection of claim 33 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement, made in the Office Action mailed on May 14, 2025 is withdrawn in view of the Amendment received on November 14, 2025, canceling the rejected claim.
Claim Rejections - 35 USC § 103
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
The rejection of claims 1, 8-10, 13, 14, 16, 17, 19-21, 24, and 32 under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Nobile et al. (US 2005/0227264 A1, published October 2005, priority January 2004) in view of Chen et al. (WO 2004/070005 A2, published August 2004), Takahashi et al. (U.S. Patent No. 7,604,938, issued October 20, 2009, priority February 2005) and Srinivasan et al. (US 2007/0275415 A1, published November 29, 2007, priority April 2006), made in the Office Action May 14, 2025 is maintained for the reasons of record.
Applicants’ arguments presented in the Amendment received on November 14, 2025 have been carefully considered but they have not been found persuasive for the reasons set forth in the, “Response to Arguments”.
The Rejection:
With regard to claim 1, Nobile et al. teach a method of detecting a nucleic acid, the method comprising the steps of:
obtaining a DNA fragment (“genomic DNA library or a cDNA library … each member of the DNA population have a common nucleic acid at the first end and a common nucleic acid at the second end … can be accomplished, for example, by ligating a first adaptor DNA sequence to one end and a second adaptor DNA sequence to a second end of each member of the DNA population … the template is about 150 bp to 750 bp in size, such as, for example about 250 bp in size”, section [0049]);
capturing the fragments onto beads (“single stranded nucleic acid template to be amplified may be attached to a capture beads … these attachments may be mediated by … oligonucleotides that are bound to the surface of the bead …”, section [0051]; “oligonucleotides can be employed which specifically hybridize to unique sequences at the end of the DNA fragment…”, section [0054]; “[e]ach capture bead is preferably designed to have a plurality of oligonucleotides that recognize … a portion of the nucleic acid template”, section [0055]);
encapsulating the beads in droplets ([c]apture beads with or without attached nucleic acid templates may be suspended in a heat stable water-in-oil emulsion…”, section [0058]; “emulsion is preferably generated by adding beads to an amplification solution …”, section [0060]; :[a]fter encapsulation of the bead and PCR solution and template DNA in the micro-reactor”, section [0065]);
conducting an amplification reaction in the droplets to yield beads carrying amplified, bead-bound nucleic acid (“the template nucleic acid may be amplified, while attached … or unattached to beads …”, section [0065]);
evaluating the contents of the droplets (“[a]fter amplification, the beads (each containing the amplified nucleic acid), may be filtered out of the emulsion flow via a bead filter … and thereafter processed for subsequent sequencing”, section [0072]); “[f]ollowing amplification of the nucleic acid templates and the attachment of the amplification copies to the bead, the beads may be recovered … beads may be isolated from the microreactors and used for sequencing”, sections [0099] and [0101]).
The nucleic acid comprises DNA (see above).
With regard to claim 8, the nucleic acid comprises an adaptor (see above).
With regard to claim 9, the droplets comprise primers (“emulsifier emulsifies a PCR reaction mixture (having a plurality of beads …”, section [0071]); “heated sections of the chips can allow for denaturation … primer annealing …”, section [0097]; see PCR reagent on sections [0113] and [0114]).
With regard to claim 10, the primers are coupled to beads (“primer species that may be immobilized on the bead”, section [0046]).
The droplets are surrounded by an immiscible fluid (“emulsion is preferably generated by adding beads to an amplification solution …”, section [0060]; :[a]fter encapsulation of the bead and PCR solution and template DNA in the micro-reactor”, section [0065]; “emulsion may be composed of discrete aqueous phase microdroplets … enclosed by a thermostable oil phase”, section [0045]).
With regard to claim 13, the amplification is PCR (section [0045], for example).
With regard to claim 16, at least about 30% of the beads capture one of the fragments (“microreactors should be sufficiently large to encompass sufficient amplification reagents for the degree of amplification required … up to about 20,000,000 or more, each containing effectively a single member of a DNA library can be suppled”, section [0062]).
With regard to claim 17, the encapsulating step produces at least about 450,000 beads liked to the fragments (see above, microreactors having 20,000,000 or more DNA library necessarily has at least 450,000 beads captured to the DNA library fragment).
The nucleic acid is genomic DNA (“emulsion amplification is a population of DNA such as, for example, a genomic DNA”, section [0049]).
With regard to claim 19, the encapsulating step results in predominantly one fragment per bead (“nucleic acid template can be diluted to obtain effectively one copy of delivered template per microreactor”, section [0068]).
With regard to claim 20, the amplification reaction result in beads carrying at least ten million copies of a unique fragment (“nucleic acid template can be diluted to obtain effectively one copy of delivered template per microreactor, and a final yield of 1,000,000 to 10,000,000 template copies per bead”, section [0068]).
With regard to claim 21, the artisans teach breaking the droplets and depositing the beads into a wells for sequencing (beads are recovered from emulsion particles, see section [0099]; and the released beads with the attached copies of template nucleic acids are deposited onto a microwells for sequencing reaction, “distribution onto multiwall (e.g., picotiter) plates”, section [0102]).
With regard to claim 24, the bead-bound nucleic acids are denatured (“beads are resuspended … and then NaOH is added to remove the annealed oligo”, section [0128]).
With regard to claim 26, the artisans explicitly teach that any amplification can be employed in their method, including isothermal amplification (“the present invention provide methods and systems for performing continuous flow amplification, specifically, encapsulated continuous flow amplification. Such embodiment may be used with thermal or isothermal amplification reactions, for example, PCR, rolling circle amplification, whole genome amplification …”, section [0010]).
While Nobile et al. explicitly teach that the DNA library are made up of small fragments such as 150 bp and 250 bp with adaptors ligated to each end of the fragments, the artisans do not explicitly state that the DNA are subject to a “fragmenting” step.
Nobile et al. while explicitly teachings performing amplification from emulsion droplets on their device via continuous flow, do not teach that a “microfluidic” chip is employed for the emulsion formation, or that they are thermocycled therein (claim 14).
Nobile et al., while explicitly teaching that the emulsion droplets should be disrupted in order to recover the amplification products therein (“method according to any claims 1-3, further comprising breaking emulsions to retrieve one or more of the amplified nucleic acid templates” (see claim 4), do not explicitly teach that the emulsion droplets are broken using a droplet-destabilizing fluid and centrifugation of the droplets.
Nobile et al. also do not explicitly state that the contents of the droplets are “electrically” evaluated.
Nobile explicitly teach that cDNA are employed for their disclosed method (“a cDNA library … each member of the DNA population have a common nucleic acid at the first end and a common nucleic acid at the second end … can be accomplished, for example, by ligating a first adaptor DNA sequence to one end and a second adaptor DNA sequence to a second end of each member of the DNA population … the template is about 150 bp to 750 bp in size, such as, for example about 250 bp in size”, section [0049]).
Chen et al. teach a method of emulsifying bead bound nucleic acids for PCR, followed by the breaking of the droplets thereafter utilizing a droplet-destabilization fluid and a centrifuge:
“Following amplification, the emulsifications were examined … Unbroken emulsions were combined into a single 1.5 ml microcentrifuge tube, while the occasional broken emulsion was discarded … the emulsion separated into two phases with a large white interface … In a chemical fume 1 ml hexanes was added to the lower phase and interface layer. The mixture was vortexed for 1 minute and centrifuged at full speed for 1 minute in a benchtop microcentrifuge. The top, oil/hexane phase was removed and discarded. After this, 1 ml of 80% Ethanol/IX Annealing Buffer was added to the remaining aqueous phase, interface, and beads” (page 23, lines 9-23)
Takahashi et al. teach an automated platform comprising a microfluidic device (“microfluidic system … result in a novel inline automated platform …”, column 9, lines 7-8), wherein encapsulated droplets are generated on a fluidic chip (“microfluidic device comprising at least one sipper, at least one fluid reservoir connected to at least one microfluidic inline reaction channel, wherein the at least one microfluidic inline channel runs through a reagent assembly area, an amplification area within a first temperature-controlled area, and a detection area within a second temperature-controlled area …”, column 9, lines 52-58; “aspirating sample droplets from the sample with a sipper into a microfluidic inline reaction channel of a microfluidic device … and forming sample plugs by mixing sample droplets with primer plugs …”, column 11, bottom to column 12, line 3; “sample plug is surrounded by an immiscible nonaqueous fluid (e.g., mineral oil) as it is being aspirated to further prevent contamination”, column 12, lines 18-21).
Takahashi et al. also teach that after amplification reaction, the droplets containing the amplified nucleic acids are sorted (“a microfluidic channel comprises a ‘valve’ downstream of the detection area, such that a decision may be made regarding whether the DNA sample plug [droplet] passing through the ‘valve’ will be aspirated, e.g., into a waste well, or selected for further analysis, e.g., with a DNA sequencing chip”, column 9, bottom to column 10, line 2), thereby evaluating the contents of the droplet.
Srinivasan et al. teach a method of amplifying nucleic acids in a droplet, wherein the artisans evidence various well-known means of detecting amplification products, such as electrical detection:
“invention provides methods, devices and systems for executing one or more droplet-based biochemical assays … amplifying nucleic acids ..”, section [0054])
“amplified nucleic acid will be detected after some number of amplification cycles … Detection generally involves using droplet operations to transport the droplet into detection zone in which a sensor measures some aspect of the droplet, such as a physical, chemical or electrical aspect, which correlate with amplification … some embodiment, the detection method for amplification is a fluorescence technique” (section [0087])
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to combine the teachings of Nobile et al. with the teachings of Chen et al., Takahashi et al. and Srinivasan et al., thereby arriving at the invention as claimed for the following reasons.
As discussed above, Nobile et al. teach a method of performing an amplification of nucleic acid template library comprising a predetermined length which are flanked by adapters on a bead inside emulsion droplets for the purpose of amplifying them therein, and collecting and sequencing the amplified products. While Nobile et al. did not perform their amplification reaction on a “fluidic chip”, the artisans explicitly taught that beads comprising oligonucleotides can be emulsified via a nozzle with extensive steps to avoid clogging of the nozzle dispensing the beads during the emulsification process (see section [0086] for example) which can be coupled to a device region for continuous thermocycling of the nucleic acids in the emulsion droplets, followed by their collection and sequencing.
Takahashi et al. also teach a method of automating the process of emulsion droplets comprising nucleic acids, wherein the emulsion products are generated within a microfluidic device and amplified therein, as well as collecting the amplified nucleic acids therein for the same purpose as suggested by Nobile et al., that is, sequencing the amplified products.
In addition, Takahashi et al. provide an additional element that allows one to sort out the droplets containing the nucleic acid amplification products from those that do not, wherein the sorting allows only those containing the amplification product to proceed to the subsequent sequencing reaction.
Therefore, one of ordinary skill in the art would have been motivated to combine the teachings of Nobile et al. with the teachings of Takahashi et al., so as to arrive at a method of encapsulating bead-bound nucleic acid templates in emulsion droplets, amplifying their contents, sorting and selecting only those droplets containing the amplified products for next taught step of sequencing reactions.
While Takahashi et al.’s taught soring method involved the detection of amplification product based on fluorescence, as evidenced by Srinivasan et al. detection of amplified product in an emulsion droplet (or bolus) by means such as optical (fluorescence), or electrical detection was routine.
Therefore, one of ordinary skill in the art would have recognized that any of such prior art known means for detecting the amplification products in a droplet for the purpose of sorting them (in the process of Takahashi et al.) would have produced the same 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.”
With regard to actively fragmenting the nucleic acids before ligating the adapters to their ends, such would have been an implicit step if not an obvious step, as it is clear from Nobile et al.’s teachings that the starting nucleic acid templates from the library should be of a certain length, which would have led the ordinarily skilled artisan to first fragment the starting nucleic acid molecules to the desired size, especially given that Nobile et al. also teach that adopters should be ligated to each of the fragments, which typically involve restriction digestion of the nucleic acids so as to produce ends which are amenable to ligation of adopters.
Lastly, Nobile et al. already teach emulsifying nucleic acids and amplifying the nucleic acids therein, followed by an explicit instruction to break the droplets for analysis of the amplified products. While Nobile et al. did not explicitly detail how the droplets should be disrupted for releasing the amplification products from the droplets, Chen et al. explicitly teach a well-known means of utilizing reagents and centrifugation means to disrupt the emulsion droplets for releasing bead bound nucleic acid amplification products.
As stated in MPEP, at 2143.02, a prior art can be modified or combined to reject claims as obvious as long as there is a reasonable expectation of success. Given that the means of disrupting emulsion droplets containing nucleic acid amplification products via use of reagents and centrifugation had already been demonstrated to work (by Chen et al.), one of ordinary skill in the art would have had a clear expectation of success at combining any of such well-known means of disrupting emulsion droplets containing amplification products therein.
Therefore, for the above reasons, the invention as claimed is prima facie obvious over the cited references.
Response to Arguments:
Applicants traverse the rejection.
Applicants state that the prior art of record does not teach or suggest an electrical detector or detecting an electrical characteristic of bead-bound nucleic acid using an electrical detector or does the Office set forth or articular the elements of a prima facie case of obviousness (page 5, Response).
On page 6 of the Response, Applicants state that a person of ordinary skill in the art would not have had a reasonable expectation of success in combining or modifying the prior art to arrive at the claimed invention.
Applicants point to various sections of Nobile (of record), Chen (of record), Takahashi (of record), Srinivasan (of record), and Kambara1 (of record) and conclude that, “[n]ot one of Nobile, Chen, Takahashi, Srinivasan, and Kambara teaches or suggest ‘an electrical detector’ as recited in claim 1,” concluding that a prima facie case of obviousness has been established (page 6, Response).
These arguments have been carefully considered but have not been found persuasive because Applicants’ arguments are based on their strictest application of the word electrical “detector” without considering what one of ordinary skill in the art would have taken from the disclosure made by Srinivasan and Takahashi specifically indicating that the “detection means” involve “optical or electrical”.
The Office reaffirms its contention that the utilization of electrical detection of nucleic acids was known in the art of molecular diagnostics, and combining such well-established means for detecting the amplicons produced in Nobile would have been predictable because bead-bound nucleic acids were released from their encapsulating emulsion droplets (thus removed from their oil surrounding medium) and placed onto a microtiter plate.
And doing so would have been well-within the conventional knowledge of the ordinary skilled artisan in question. This is plainly evidenced by Srinivasan et al. who simply state that the detection means can be in an optical or electrical signal form:
“nucleic acid amplification followed by an affinity-based assay that results in optical or electrical signal” (section [0281])
“droplet microactuator system of the invention makes use of a variety of optical detection approaches. A droplet microactuator and/or system of the invention may include one or more electrochemical sensors arranged to sense a property of a droplet …” (section [0522])
As well, Takahashi also evidences that the use of optical or electrical means for detecting amplicons is so well-known that no additional explanation is necessary:
“The detection area of microfluidic device of the invention allows signals from amplified DNA products to be monitored. Detection may be based on optical, chemical, electrochemical, thermal or other properties of the amplified DNA products.” (column 38, lines 36-38)
While Applicants attempt to make much of the word, “detector” of the term, “electrical detector,” when viewing the explicit suggestion that when amplification products are assayed based on an optical or electrical signal, or electrochemical sensor (as suggested by Srinivasan) or that the detection area allows the signals to be detected based on “optical, chemical, electrochemical … or other properties”, one of ordinary skill in the art would have recognized that the detector must be commensurate with the type of signal being assayed for.
In addition, Applicants are also advised that their own specification does not make much of what an electrical detection or detector is, but disclose it as just a known alternative.
As a matter of fact, much of Applicants’ own specification, when pertaining to an electrical property, discusses them in the electromotive force of the droplets, not for the detection of the amplified products in after the droplets are burst and recovered onto a detection module (see sections [0008], [0009], [0016], [0070], etc.).
When it comes to the actual detectors of the amplified nucleic acids, Applicants’ own specification discusses them in the same generic way, and only describes optical detection means:
“The detection apparatuses can be optical or electrical detectors or combinations thereof. Example of suitable apparatuses include optical waveguides, microscopes, diodes, light simulating devices (e.g., lasers), photomultiplier tubes, and processors (e.g., computers and software), and combinations therefor, which cooperate to detect a signal representative of a characteristic, marker, or reporter, and to determine and direct the measurement or the sorting action at the sorting module. However, other detection techniques can also be employed” (section [0205])
Taking Applicants’ disclosure as a whole, it would appear that the specification is more interested in the optical detection means (as demonstrated above where no actual electrical detector types are listed) and that the electrical detector is just an obvious known alternative detection means known at the time the invention was made.
Indeed, this is evidenced by Applicants’ own specification:
“A preferred detector is an optical detector, such as a microscope, which may be coupled with a computer and/or other image processing or enhancement devices to process images or information produced by the microscope using known techniques.” (section [0218])
Therefore, the Office is not convinced that the electrical detector means is anything other than an obvious alternative known detection means that needed no additional disclosure (as evidenced by Applicants’ own lack of description), as well as being well-known that the suggestion made by Srinivasan would have been enough motivation to realize a predictable outcome using an electrical detector, to detect the “electrical signal” produced from the amplification products.
For these reasons, Applicants’ arguments are not found convincing and the rejection is maintained.
The rejection of claim 25 under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Nobile et al. (US 2005/0227264 A1, published October 2005, priority January 2004) in view of Chen et al. (WO 2004/070005 A2, published August 2004), Takahashi et al. (U.S. Patent No. 7,604,938, issued October 20, 2009, priority February 2005) and Srinivasan et al. (US 2007/0275415 A1, published November 29, 2007, priority April 2006), as applied to claims 1, 8-10, 13, 14, 16, 17, 19-21, 24, and 32 above, and further in view of Kambara et al. (US 2001/0024790 A1, published September 27, 2001), made in the Office Action May 14, 2025 is maintained for the reasons of record.
Applicants’ arguments for the instant rejection had been grouped in their arguments directed toward the rejection over Nobile, Chen, Takahashi, and Srinivasan, which have been responded to above.
As no other separate arguments are made for this rejection, the rejection is maintained for the reasons of record and arguments presented above.
The Rejection:
The teachings of Nobile et al., Chen et al., Takahashi et al. and Srinivasan et al. have already been discussed above.
While the artisans all teach that the bead bound amplification products produced in the emulsion droplets should be sequenced, the artisans do not explicitly teach all possible known means of sequencing the amplification products.
Kambara et al. teach a method of pyrosequencing nucleic acids simultaneously on a chip, wherein the artisans explicitly state that the target nucleic acids to be sequenced are immobilized on a bead (“primers are immobilized on a solid surface, beads or the like, and the target DNA is obtained by hybridizing a double-stranded DNA sample with these primers”, section [0010]), wherein the sequencing reagents, such as polymerases, can be provided on a bead, immobilized thereon (“[i]n this case, DNAs to be sequenced are immobilized on the beads, but enzyme, such as luciferase, can also be additional immobilized on the same beads …”, section [0082]).
It would have been prima facie obvious to one of ordinary at the time the invention was made to combine the teachings of Nobile et al., Chen et al., Takahashi et al. and Srinivasan et al. with the teachings of Kambara et al., thereby arriving at the invention as claimed for the following reasons.
One of ordinary skill in the art would have had a reasonable expectation of success at delivering the bead-bound, amplification products to any sequencing platform in the art as Nobile, Chen et al., Takahashi et al. and Srinivasan et al. suggested.
Therefore, one of ordinary skill in the art would have been motivated to deliver the amplified products produced from the combination of Nobile et al., Chen et al., Takahashi et al., and Srinivasan et al. onto the sequencing platform of Kambara et al. for the purpose of sequencing them by pyrosequencing means, a technique well-established at the time the invention was made.
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. 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.
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/YOUNG J KIM/Primary Examiner
Art Unit 1637 February 13, 2026
/YJK/
1 Kambara was relied upon for the rejection of claim 25. Applicants’ inclusion of all of the references in a single argument has been taken to mean that arguments grouped the two rejections into one.