DETAILED ACTION
Applicant's response, filed 09/12/2025, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. Herein, "the previous Office action" refers to the Non-Final Rejection of 06/12/2025.
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 .
Status of the Claims
Claims 1-20 are examined.
Priority
This application with filling date (12/16/2021) claims priority from US Application No. 63/132,479 (12/31/2020) as reflected in the filing receipt mailed on Feb. 25, 2022. The claims to the benefit of priority are acknowledged. As detailed on the 02/25/2022 filing receipt, the application claims priority as early as 12/31/2020. The effective filing date of claims 1-20 is 12/31/2020.
Response to applicant's remarks in regards of Priority
The Remarks of 09/12/2025 have been fully considered but are not persuasive for the reasons below:
Applicant asserts “Applicant respectfully disagrees with the Examiner's priority determination and submits that all claims are fully supported by the priority document and are entitled to the effective date of 12/31/2020” – pg. 1 para. 2. The argument is persuasive regarding the argued priority.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 10/31/2025 was considered.
Claim Interpretation
Claim 1 recites “identifier associated with the source” being interpreted as any labeling mechanism that allows the identification of the referred nucleic acid.
Withdrawal / Revision of Objections and/or Rejections
In view of the amendment and remarks from 09/12/2025, the rejection of claims 1-20 under 35 USC § 112(b) is hereby withdrawn in view of Applicant's amendments.
The rejection of claims 1-3, 6-10, 12-18 and 20 under 35 U.S.C. 103(a) as being unpatentable over Giddings and Macaulay is hereby withdrawn in view of Applicant's amendments due to the persuasive arguments that this combination of references doesn’t teach the claimed method.
The following rejections and/or objections are either maintained or newly applied for claims 1-20. They constitute the complete set applied to the instant application.
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 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 negated by the manner in which the invention was made. The factual inquiries for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 1,10, 12-13, 17-18 and 20 are rejected under 35 U.S.C. 103(a) as being unpatentable over US Application 2020/0075130 – referred to in the action as Shankar – in view of Macaulay et. al. “Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq” Nature Protocols 11:2081–2103 (2016) – referred to in the action as Macaulay – as evidenced by Kupiec et. al. “Quality-Control Analytical Methods: High-Performance Liquid Chromatography” Int J Pharm Compd. 8(3):223-7 (2004) – referred to in the action as Kupiec.
Determination of the Scope and Content of the Prior Art
(MPEP §2141.01)
Independent claim 1 recites “a method for determining a sequence of nucleic acids, the method comprising: extracting nucleic acids from a sample with a purification instrument in accordance with a purification plan of a run plan, the purification plan including an identifier associated with a source … automatically transferring the transfer file to the sequencing instrument; and sequencing at least a portion of the extracted nucleic acids with the sequencing instrument in accordance with a sequencing plan of the run plan and based on the transfer file, the sequencing plan including the identifier associated with the source and indicating an assay to be used with the extracted nucleic acids associated with the source”. However, Shankar teaches a method for user guided initiating of an instrument includes receiving a run plan via a user interface of the instrument; indicating on the user interface, based on the run plan, a consumable to be provided to the instrument; detecting the presence of the consumable using a vision system; and indicating the presence of the consumable via the user interface (Abstract); wherein the management module of the instrument comprises a sequencing module and a control module ([0041] and Fig. 4); wherein the system can receive a run plan (i.e. reading on the use of transfer files) for performing a particular test or tests (i.e. reading on indication of an assay) [0050]; wherein the system includes a nucleic acid sequencing instrument to generate a sequencing run [0003]; reading on the recited limitation in claim 1.
Dependent claim 10 recites “wherein the sequencing plan includes a reference to an assay definition”. Shankar teaches a method for user guided initiating of an instrument includes receiving a run plan via a user interface of the instrument (Abstract); wherein the system can receive a run plan for performing a particular test or tests (i.e. reference to an assay definition) [0050]; reading on claim 10.
Dependent claim 12 recites “wherein the sequencing plan associates a nucleic acid tag or barcode with the identifier associated with the source”. Shankar teaches a method for user guided initiating of an instrument includes receiving a run plan via a user interface of the instrument (Abstract); wherein the system can recognize a barcode of a sample and determine that the consumable has been used in a previous run [0048]; reading on claim 12.
Dependent claim 13 recites “wherein preparing the run plan includes preparing the run plan on the sequencing instrument”. However, Shankar teaches a method for user guided initiating of an instrument includes receiving a run plan via a user interface of the instrument (Abstract); wherein a vision system is used within a sequencing instrument, to assist the user in preparing the instrument to run a test [0031]; reading on claim 13.
Dependent claim 18 recites “determining automatically with the sequencing instrument a presence of sequencing consumables consistent with the sequencing plan”. However, Shankar teaches a method for user guided initiating of an instrument includes receiving a run plan via a user interface of the instrument; indicating on the user interface, based on the run plan, a consumable to be provided to the instrument; detecting the presence of the consumable using a vision system; and indicating the presence of the consumable via the user interface (Abstract); wherein the management module of the instrument comprises a sequencing module and a control module ([0041] and Fig. 4); reading on claim 18.
Dependent claim 20 recites “providing a sequencing progress update associated with the run plan from the sequencer to a server. However, Shankar teaches a method for user guided initiating of an instrument includes receiving a run plan via a user interface of the instrument; indicating on the user interface, based on the run plan, a consumable to be provided to the instrument; detecting the presence of the consumable using a vision system; and indicating the presence of the consumable via the user interface (Abstract); wherein the display can be further used to indicate the progress of various steps of a run plan [0095]; reading on claim 20.
Ascertainment of the Difference Between Scope the Prior Art and the Claims (MPEP §2141.02)
Regarding claim 1, Shankar does not explicitly teach “disposing the extracted nucleic acids disposed in a transfer plate following purifying, a well location of the extracted nucleic acids being stored in a transfer file associating the well location on the transfer plate with the identifier; transferring the transfer plate to a sequencing instrument”. However, Macaulay teaches a method that allows parallel sequencing of the genome and transcriptome of a single cell (pg. 2081 col. 2 para. 1); wherein genomic DNA is purified (pg. 2083 col. 1 para. 3) collected and transferred to a new plate for further sequencing (pg. 2082 col. 2 para. 1 and Fig. 1); wherein sequencing steps are performed in sequencers (i.e. transferring the plate to a sequencing instrument) (pg. 2084 col. 1 para. 3); wherein single cells can be isolated in multiwell plates (pg. 2081 col. 1 para. 4); and files store information from the single-cell paired-end sequencing (pg. 2096 para. 79); reading on the recited limitations in claim 1.
Regarding claim 17, Shankar does not explicitly teach “determining automatically with the purification instrument a presence of purification consumables consistent with the purification plan”. However, Macaulay teaches the HPLC detector is used to sense the presence of a compound passing through and to provide an electronic signal to a data-acquisition device pg. 225 col. 1 para. 2 Kupiec; reading on claim 17.
Finding of Prima Facie Obviousness Rationale and Motivation
(MPEP §2142-2143)
Regarding claims 1, 10, 12-13, 17-18 and 20 ; it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to incorporate the teachings by Macaulay to the method for user guided initiating of an instrument includes receiving a run plan via a user interface of the instrument; indicating on the user interface as taught by Shankar to dispose the extracted nucleic acids disposed in a transfer plate following purifying, a well location of the extracted nucleic acids being stored in a transfer file associating the well location on the transfer plate with the identifier; transfer the transfer plate to a sequencing instrument; including an identifier associated with a second source different than the initial one and an indication of a second type of nucleic acids to extract; request with the purification instrument the set of run plans and displaying the set of run plans with the purification instrument; receive a selection of the run plan from a user of the purification instrument and determine automatically with the purification instrument a presence of purification consumables consistent with the purification plan. One of ordinary skill in the art would be motivated to apply the teachings by Macaulay to the method by Shankar to robustly generate full-length transcriptome data and genomic DNA sequences (pg. 2081 col. 2 para. 2 Macaulay). One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for nucleic acids sequencing.
Claims 2-3, 6-9, and 14-16 are rejected under 35 U.S.C. 103(a) as being unpatentable over Shankar and Macaulay as applied above to claims 1 and 13 further in view of Giddings et. al. “A Software System for Data Analysis in Automated DNA Sequencing” Genome Res. 8(6):644–665 (1998) – referred to in the action as Giddings.
Determination of the Scope and Content of the Prior Art
(MPEP §2141.01)
Dependent claim 2 recites “wherein a concentration of the extracted nucleic acids is stored in the transfer file”. Dependent claim 3 recites “transferring the transfer file to a server, wherein transferring the transfer file to the sequencing instrument includes transferring the transfer file from the server to the sequencing instrument”. Dependent claim 6 recites “preparing the run plan, the run plan including the purification plan and the sequencing plan”. Dependent claim 7 recites “wherein the purification plan includes an indication of a type of nucleic acids to extract”. Dependent claim 14 recites “storing the run plan with a set of run plans”.
Macaulay teaches parallel sequencing of a single cell’s genome and transcriptome involving a method for physical separation (i.e. purification plan) of the DNA and RNA (i.e. second type of nucleic acid to extract different than the other source) (pg. 2081 para. 1); wherein the RNA separation was performed with oligo-dt30Vn-labeled beads (i.e. identifier associated with the second source); reading on claims 8-9.
Macaulay teaches a method that allows parallel sequencing of the genome and transcriptome of a single cell (pg. 2081 col. 2 para. 1); wherein high pressure liquid chromatography (HPLC) instrument with automated liquid handling protocols were used to purify nucleic acids; wherein said instrument displays data obtained from the run as evidenced by Kupiec (pg. 224 Fig. 1) (i.e. displaying the set of run plans with the purification instrument) (pg. 2085 col.1); reading on claim 15.
Macaulay teaches that a protocol can be performed manually on small numbers of samples; however, if numerous single cells are to be analyzed, it is advised the use of automated liquid-handling platforms during the purification runs in the HPLC instrument (pg. 2085 col.1) for users with experience in the programming and operation of liquid-handling robots (i.e. selection of the run plan from a user); wherein the instrument offers the choice of methods to be selected as evidenced by Kupiec (pg. 225 col. 2 para. 4); reading on claim 16.
Ascertainment of the Difference Between Scope the Prior Art and the Claims (MPEP §2141.02)
Regarding claim 2, neither Shankar nor Macaulay teach the limitation above. Giddings teaches collections of files stored within a directory within the Base Finder software being saved and loaded in aggregate to allow simple multi trace processing (pg. 648 col. 2 para. 5); wherein the data represent the dye-linked DNA fragment concentration (a concentration of the extracted nucleic acids) versus time for each of the four different dyes, with one channel per dye (pg. 654 col. 1 para. 3); reading on claim 2.
Regarding claim 3, neither Shankar nor Macaulay teach the limitation above. Giddings teaches a distributed client/server approach via an interface made available as a server to the network, accepting requests from remote objects (pg. 647 col. 2 para. 3); processing each request and outputting a lmark (lane marker) file (pg. 648 col.1 para. 1); to be used as an component of the sequencing process in slab-gel-based systems (pg. 648 col. 2 para. 3); reading on claim 3.
Regarding claim 6, neither Shankar nor Macaulay teach the limitation above. Giddings teaches sequencing runs including lane finding (for slab gel electrophoresis), base-calling, assembly, and finishing (pg. 645 col. 1 para. 2); wherein DNA separation (i.e. purification) and detection steps are performed in a fluorescence-based gel electrophoresis instrument (i.e. purification plan) (pg. 633 col. 2 para. 3); reading on claim 6.
Regarding claim 7, neither Shankar nor Macaulay teach the limitation above. Giddings teaches a powerful scripting capabilities combined with modularity and multilane handling allow the user to customize any type of trace processing (i.e. indication of a type of nucleic acids to extract)(pg. 637 para. 1); reading on claim 7.
Regarding claim 14, neither Shankar nor Macaulay teach the limitation above. Giddings teaches a scripting mechanism that provides means by which a sequence of tool-based processing steps can be applied to the data in an automated way (pg. 650 col. 1 para. 3); with an user interface that allows the definition of scripts that specify the complete set of steps for processing data from particular instrument configurations (pg. 649 col. 1 para. 1); wherein the program allows the saving of defined scripts (pg. 651 col. 1 para. 4; reading on claim 14.
Finding of Prima Facie Obviousness Rationale and Motivation
(MPEP §2142-2143)
Regarding claims 2-3, 6-9, and 14-16; it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to incorporate the teachings by Giddings to the method for user guided initiating of an instrument includes receiving a run plan via a user interface of the instrument; indicating on the user interface as taught by Shankar and Macaulay to incorporate a concentration of the extracted nucleic acids stored in the transfer file; transferring the transfer file to a server, wherein transferring the transfer file to the sequencing instrument includes transferring the transfer file from the server to the sequencing instrument; preparing the run plan, the run plan including the purification plan and the sequencing plan; including an indication of a type of nucleic acids to extract; and storing the run plan with a set of run plans. One of ordinary skill in the art would be motivated to apply the teachings by Giddings to the method by Shankar and Macaulay to improve the preprocessing capabilities and stability, as well as the performance of the base-calling algorithm with the goal of fully hands-off, automated processing (pg. 663 col. 1 para. 1 Giddings). One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for nucleic acids sequencing.
Claims 4-5 are rejected under 35 U.S.C. 103(a) as being unpatentable over Shankar and Macaulay as applied to claim 1 above further in view of Alberti et. al. “Data Descriptor: Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition” Sci. Data 4, 170093 (2017) – referred to in the action as Alberti.
Determination of the Scope and Content of the Prior Art
(MPEP §2141.01)
Dependent claim 4 recites “disposing portions of the extracted nucleic acids in an archive plate”. Dependent claim 5 recites “storing locations of the portions on the archive plate in the transfer file”.
Ascertainment of the Difference Between Scope the Prior Art and the Claims
(MPEP §2141.02)
Regarding claims 4-5, neither Shankar nor Macaulay teach the recited limitations. However, Alberti teaches some nucleic acids extractions being used for library preparation and sequencing process and other nucleic acids extractions being stored as a backup (pg. 6 para. 3); wherein backup plates were stored frozen at −80 °C (pg. 7 para. 1) (i.e. disposing portions of the extracted nucleic acids in an archive plate); wherein a sample management system records the storage location and monitors sample usage (pg. 3 para. 2); reading on claims 4-5.
Finding of Prima Facie Obviousness Rationale and Motivation
(MPEP §2142-2143)
Regarding claims 4-5; it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to incorporate the teachings by Alberti to the method for user guided initiating of an instrument includes receiving a run plan via a user interface of the instrument; indicating on the user interface as taught by Shankar and Macaulay to dispose portions of the extracted nucleic acids in an archive plate and store locations of the portions on the archive plate in the transfer file. One of ordinary skill in the art would be motivated to apply the teachings by Alberti to the method by Shankar and Macaulay to optimize protocols applied to processing of samples (pg. 8 para. 5 Alberti). One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for nucleic acids sequencing.
Claim 11 are rejected under 35 U.S.C. 103(a) as being unpatentable over Shankar and Macaulay as applied to claim 1 above further in view of Paegel et. al. “Microchip Bioprocessor for Integrated Nanovolume Sample Purification and DNA Sequencing” Anal. Chem. 74, 5092-5098 (2002) – referred to in the action as Paegel.
Determination of the Scope and Content of the Prior Art
(MPEP §2141.01)
Dependent claim 11 recites “wherein the sequencing plan includes a reference to sequencing chip”.
Ascertainment of the Difference Between Scope the Prior Art and the Claims
(MPEP §2141.02)
Regarding claim 11, neither Shankar nor Macaulay teach the recited limitation. However, Paegel teaches a microchip bioprocessor for integrated DNA sequencing (pg. 5092 para. 1); wherein sequencing data is obtained from the on-chip oligonucleotide capture-purified sample (pg. 5098 Fig. 5); reading on claim 11.
Finding of Prima Facie Obviousness Rationale and Motivation
(MPEP §2142-2143)
Regarding claim 11; it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to incorporate the teachings by Paegel to the method for user guided initiating of an instrument includes receiving a run plan via a user interface of the instrument; indicating on the user interface as taught by Shankar and Macaulay to include a reference to sequencing chip in the sequencing plan. One of ordinary skill in the art would be motivated to apply the teachings by Paegel to the method by Shankar and Macaulay to provide state-of-the art sequencing results (pg. 5092 col. 1 para. 1 Paegel). One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for nucleic acids sequencing.
Claim 19 are rejected under 35 U.S.C. 103(a) as being unpatentable over Shankar and Macaulay as applied to claim 1 above further in view of Liu et. al. “High-Throughput Purification Platform in Support of Drug Discovery” ACS Comb. Sci. 14(1):51-9 (2012) – referred to in the action as Liu.
Determination of the Scope and Content of the Prior Art
(MPEP §2141.01)
Dependent claim 19 recites “providing a purification progress update associated with the run plan from the purification instrument to a server”.
Ascertainment of the Difference Between Scope the Prior Art and the Claims
(MPEP §2141.02)
Regarding claim 19, neither Shankar nor Macaulay teach the recited limitation. However, Liu teaches a high throughput purification platform (pg. 51 para. 1); wherein data is saved on the server for chemists to review and to import to the electronic notebook (pg. 56 col. 2 para. 1); reading on claim 19.
Finding of Prima Facie Obviousness Rationale and Motivation
(MPEP §2142-2143)
Regarding claim 19; it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to incorporate the teachings by Liu to the method for user guided initiating of an instrument includes receiving a run plan via a user interface of the instrument; indicating on the user interface as taught by Shankar and Macaulay to dispose portions of the extracted nucleic acids in an archive plate and store locations of the portions on the archive plate in the transfer file. One of ordinary skill in the art would be motivated to apply the teachings by Liu to the method by Shankar and Macaulay to explore the relevant chemical space in a rapid and efficient manner(pg. 58 col. 2 para. 1 Liu). One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for nucleic acids purification.
Regarding automating a manual activity, MPEP 2144.04 (III) discusses the obvious to automate rationale in regards to automating a manual activity. In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958) (Appellant argued that claims to a permanent mold casting apparatus for molding trunk pistons were allowable over the prior art because the claimed invention combined "old permanent-mold structures together with a timer and solenoid which automatically actuates the known pressure valve system to release the inner core after a predetermined time has elapsed." The court held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art.).
Response to applicant's remarks in regards of Claim Rejection 35 U.S.C. ~ 103
The Remarks of 09/12/2025 have been fully considered but are not persuasive for the reasons below:
Regarding the applicant’s arguments, all arguments are persuasive; the Examiner have cited new art to address the recitations.
Conclusion
No claims are allowed.
Regarding 35 U.S.C. § 101, claims 1-20 are patent eligible because claimed invention recites the integral use of a machine to achieve performance of a method (i.e. a run plan that includes instructions for purification and sequencing and are then executed according to the plan); which integrates the recited judicial exception into a practical application.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FRANCINI A FONSECA LOPEZ whose telephone number is (571)270-0899. The examiner can normally be reached Monday - Friday 8AM - 5PM ET.
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.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached at (571) 272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/F.F.L./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685