DETAILED ACTION
Notice of 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 .
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 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.
Status of the Claims
Claims 1-20 are pending.
Claims 1-20 are rejected.
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.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 04/17/2026 was considered.
Withdrawal / Revision of Objections and/or Rejections
Applicant's response, filed 04/16/2026, has been fully considered. 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
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.
A. Claims 1, 10, 12-13, 17-18 and 20 are rejected under 35 U.S.C. 103(a) as being unpatentable Shankar (US Application 2020/0075130) in view of Cario ("Samasy: an automated system for sample selection and robotic transfer." Biotechniques 65(6):357-360 (2018)) in view of Macaulay (“Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq” Nature Protocols 11:2081–2103 (2016)) as evidenced by Kupiec (“Quality-Control Analytical Methods: High-Performance Liquid Chromatography” Int J Pharm Compd. 8(3):223-7 (2004)), as cited on the 06/12/2025 Form PTO-892.
Claim 1 recites:
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 of the sample;
…
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
• 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].
automatically transferring the transfer file to the sequencing instrument … disposing the extracted nucleic acids 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;
• Shankar does not teach the recitation above. However, Cario teaches a visual web-based sample management system for 96-well plates with support for automated robotic transfer (pg. 357 col. 3 para. 2); wherein Figure 1 shows a transfer file sample that enables the user to find sample information, a search box is provided that will fuzzy match values (i.e. identifier) in any attribute field – which includes well location (pg. 358 Fig. 1); wherein the model is applied for sample management in sequencing systems (pg. 359 col. 1 para. 5).
transferring the transfer plate to a sequencing instrument
• Shankar does not teach the recitation above. 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).
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].
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].
Claim 13 recites:
wherein preparing the run plan includes preparing the run plan on the sequencing instrument
• 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].
Claim 17 recites:
further comprising determining automatically with the purification instrument a presence of purification consumables consistent with the purification plan
• Shankar does not teach the recitation above. 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.
Claim 18 recites:
further comprising determining automatically with the sequencing instrument a presence of sequencing consumables consistent with the sequencing plan
• 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).
Claim 20 recites:
further comprising providing a sequencing progress update associated with the run plan from the sequencer to a server.
• 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 display can be further used to indicate the progress of various steps of a run plan [0095].
Rationale for combining (MPEP §2142-2143)
Regarding claims 1, 10, 12-13, 17-18 and 20, 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, in the course of routine experimentation and with a reasonable expectation of success, the methods of Shankar in view of Cario and Macaulay because all references disclose methods for nucleic acids sequencing. The motivation would have been to robustly generate full-length transcriptome data and genomic DNA sequences (pg. 2081 col. 2 para. 2 Macaulay) and to incorporate the construction of a sample database, intuitive display of sample and batch information, and facilitation of automated sample transfer or subset (pg. 357 Abstract Cario)
Therefore it would have been obvious to one of ordinary skill in the art to substitute the nucleic acids sequencing method of Shankar to the methods by Cario and Macaulay because such a substitution is no more than the simple substitution of one known element for another. 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.
B. Claims 2-3, 6-9 and 14-16 are rejected under 35 U.S.C. 103(a) as being unpatentable Shankar, Cario and Macaulay as applied to claims 1 and 13 above further in view of Giddings (“A Software System for Data Analysis in Automated DNA Sequencing” Genome Res. 8(6):644–665 (1998)), as cited on the 06/12/2025 Form PTO-892.
Claim 2 recites:
wherein a concentration of the extracted nucleic acids is stored in the transfer file
• Neither Shankar or Cario or Macaulay teach the recitation above. However, 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 (i.e. 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);
Claim 3 recites:
further comprising 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
• Neither Shankar or Cario or Macaulay teach the recitation above. However, 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 (i.e. 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).
Claim 6 recites:
further comprising preparing the run plan, the run plan including the purification plan and the sequencing plan
• Neither Shankar or Cario or Macaulay teach the recitation above. However, Giddings teaches sequencing runs including lane finding (i.e. 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. reading on steps that follows a purification plan) (pg. 633 col. 2 para. 3).
Claim 7 recites:
wherein the purification plan includes an indication of a type of nucleic acids to extract.
• Neither Shankar or Cario or Macaulay teach the recitation above. However, 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).
Claim 8 recites:
wherein the purification plan includes an identifier associated with a second source and an indication of a second type of nucleic acids to extract.
• 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).
Claim 9 recites:
wherein the type of nucleic acids and the second type of nucleic acids are different.
• 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) (pg. 2101 Table 1).
Claim 14 recites:
further comprising storing the run plan with a set of run plans
• Neither Shankar or Cario or Macaulay teach the recitation above. However, 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.
Claim 15 recites:
further comprising requesting with the purification instrument the set of run plans and displaying the set of run plans with the purification instrument
• 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 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).
Claim 16 recites:
further comprising receiving a selection of the run plan from a user of the purification instrument
• 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).
Rationale for combining (MPEP §2142-2143)
Regarding claims 2-3, 6-9 and 14-16, 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, in the course of routine experimentation and with a reasonable expectation of success, the methods of Shankar, Cario and Macaulay in view of Giddings because all references disclose methods for nucleic acids sequencing. The motivation would have been 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).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the nucleic acids sequencing method of Shankar, Cario and Macaulay to the methods by Giddings because such a substitution is no more than the simple substitution of one known element for another. 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.
C. Claims 4-5 are rejected under 35 U.S.C. 103(a) as being unpatentable Shankar, Cario and Macaulay as applied to claim 1 above further in view of Alberti (“Data Descriptor: Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition” Sci. Data 4, 170093 (2017)), as cited on the 06/12/2025 Form PTO-892.
Claim 4 recites:
further comprising disposing portions of the extracted nucleic acids in an archive plate
• Neither Shankar or Cario or Macaulay teach the recitation above. 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).
Claim 5 recites:
further comprising storing locations of the portions on the archive plate in the transfer file
• Neither Shankar or Cario or Macaulay teach the recitation above. 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 (i.e. reading on transfer files) (pg. 3 para. 2).
Rationale for combining (MPEP §2142-2143)
Regarding claims 4-5, 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, in the course of routine experimentation and with a reasonable expectation of success, the methods of Shankar, Cario and Macaulay in view of Alberti because all references disclose methods for nucleic acids sequencing. The motivation would have been to optimize protocols applied to processing of samples (pg. 8 para. 5 Alberti).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the nucleic acids sequencing method of Shankar, Cario and Macaulay to the methods by Alberti because such a substitution is no more than the simple substitution of one known element for another. 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.
D. Claim 11 is rejected under 35 U.S.C. 103(a) as being unpatentable Shankar, Cario and Macaulay as applied to claim 1 above further in view of Paegel (“Microchip Bioprocessor for Integrated Nanovolume Sample Purification and DNA Sequencing” Anal. Chem. 74, 5092-5098 (2002)),as cited on the 06/12/2025 Form PTO-892.
Claim 11 recites:
wherein the sequencing plan includes a reference to sequencing chip
• Neither Shankar or Cario or Macaulay teach the recitation above. 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).
Rationale for combining (MPEP §2142-2143)
Regarding claims 1, 10, 12-13, 17-18 and 20, 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, in the course of routine experimentation and with a reasonable expectation of success, the methods of Shankar, Cario and Macaulay in view of Paegel because all references disclose methods for nucleic acids sequencing. The motivation would have been to provide state-of-the art sequencing results (pg. 5092 col. 1 para. 1 Paegel).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the nucleic acids sequencing method of Shankar, Cario and Macaulay to the methods by Paegel because such a substitution is no more than the simple substitution of one known element for another. 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.
E. Claim 19 is rejected under 35 U.S.C. 103(a) as being unpatentable Shankar, Cario and Macaulay as applied to claim 1 above further in view of Liu (“High-Throughput Purification Platform in Support of Drug Discovery” ACS Comb. Sci. 14(1):51-9 (2012)) as cited on the 06/12/2025 Form PTO-892.
Claim 19 recites:
further comprising providing a purification progress update associated with the run plan from the purification instrument to a server
• Neither Shankar or Cario or Macaulay teach the recitation above. 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).
Rationale for combining (MPEP §2142-2143)
Regarding claim 19, 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, in the course of routine experimentation and with a reasonable expectation of success, the methods of Shankar, Cario and Macaulay in view of Liu because all references disclose methods for nucleic acids sequencing. The motivation would have been to explore the relevant chemical space in a rapid and efficient manner(pg. 58 col. 2 para. 1 Liu).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the nucleic acids sequencing method of Shankar, Cario and Macaulay to the methods by Liu because such a substitution is no more than the simple substitution of one known element for another. 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.
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 regard to Claim Rejection 35 U.S.C. ~ 103
The Remarks of 04/16/26 have been fully considered but are not persuasive for the reasons below:
Applicant asserts starting in pg. 6-7:
Shankar does not teach a purification plan as recited in claim 1. Claim 1 specifically requires "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 of the sample." Shankar is directed to automated monitoring of preparation tasks and verification of appropriate reagents for instruments. Shankar's run plan relates to consumable verification and instrument setup, not to a purification plan that includes an identifier associated with a source of the sample as required by claim 1. Shankar does not teach extracting nucleic acids from a sample with a purification instrument in accordance with a purification plan, disposing extracted nucleic acids in a transfer plate, and storing locations and identifiers in a transfer file. Similarly, Macaulay does not teach the transfer file as recited in claim 1. Claim 1 requires "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." While Macaulay teaches transferring supernatant containing gDNA to a new 96-well plate and instructs to "keep track of the address of each cell," Macaulay does not teach storing this information in a transfer file that associates the well location on the transfer plate with an identifier associated with a source of the sample. Macaulay's instruction to "keep track of the address of each cell" is merely a general laboratory practice and does not constitute a transfer file as claimed. Additionally, neither Shankar nor Macaulay teaches "automatically transferring the transfer file to the sequencing instrument" as recited in claim 1. The claimed method requires that a transfer file, which stores the well location of the extracted nucleic acids and associates that well location with an identifier, be automatically transferred to the sequencing instrument. No such automatic file transfer is disclosed in either reference. Furthermore, Applicant respectfully submits that Shankar does not teach sequencing in accordance with a sequencing plan of a run plan and based on the transfer file, in which the sequencing plan and transfer file include the identifier associated with the source as required by claim 1. While Shankar teaches that the system can receive a run plan for performing a particular test or tests, Shankar does not teach sequencing in accordance with the sequencing plan and transfer file with the form as claimed
It is respectfully submitted that the argument related to Shankar not teaching the "well location of the extracted nucleic acids being stored in a transfer file associating the well location on the transfer plate with the identifier" is persuasive. This is a second Non-Final examination that now describes teachings by Cario regarding said limitation, which also addressed the automated transferring step.
Regarding the automation of the files transferring step, 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.
The detailed explanation of subject matter suggested by a prior art reference is entirely acceptable when establishing a rationale for obviousness: "to support the conclusion that the claimed invention is directed to obvious subject matter, either the references must expressly or impliedly suggest the claimed invention or the examiner must present a convincing line of reasoning as to why the artisan would have found the claimed invention to have been obvious in light of the teachings of the references" (Ex parte Clapp, 227 USPQ 972 at 973 (BPAI 1985)); "Office personnel may also take into account 'the inferences and creative steps that a person of ordinary skill in the art would employ' (KSR v. Teleflex Inc., 82 USPQ2d 1385 at 1396 (SC 2007))" (MPEP 2141 § 11.C); "the rationale to support a rejection under 35 U.S.C. 103 may rely on logic and sound scientific principle" (MPEP 2144.02). The examiner's explanation of how the combination of teachings read over the claimed invention presents a convincing line of reasoning, takes into account and explains the inferences and creative steps by a person of ordinary skill in the art, and relies on logic and sound scientific principle.
Conclusion
No claims are allowed.
Regarding 35 U.S.C. § 101, claims 1-20 appear to be 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.
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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.
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/F.F.L./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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