Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Status
Claims 1-20 are pending.
Claims 1-20 are rejected.
Priority
The instant application filed on 26 September 2022 claims domestic priority to provisional application 63/293,587 filed 23 December 2021. As such, the effective filing date of claims 1-20 is 23 December 2021.
Information Disclosure Statement
All IDSs were considered by the examiner.
Drawings
There are two sets of drawings in the application: listed as DRW.NONBW (Figures 1-12) and DRW.SUPP (Figures 1-24). Clarification should be provided as to which is the correct set. The examiner is referencing the drawings listed as DRW.NONBW which includes Figures 1-12.
The drawings are objected to under 37 CFR 1.83(a) because they fail to show in Figure 1:
The sequencing device 114 bypasses the network 112 and communicates directly with …the client device 108. [0042]
The server device(s) 102 may also communicate with the client device 108. [0043]
The database 116 also stores one or more models, such as the variant analysis model 107. [0052]
The components of environment 100 can also communicate directly with each other, bypassing the network 112…the client device 108 communicates directly with the sequencing device 114. [0053]
the client device 108 communicates directly with the diagnostic workflow system 106. [0053]
as described in the specification. Any structural detail that is essential for a proper understanding of the disclosed invention should be shown in the drawing. MPEP § 608.02(d). Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 8, and 15, and dependent claims 2-7, 9-14, and 16-20, are rejected under 35 U.S.C. 103 as being unpatentable over Illumina Document# 1000000141465v00 (Illumina DRAGEN Bio-IT Platform 3.7 User Guide, October 2020, pages 1-308) in view Illumina Technical Note: Sequencing (BaseSpace Sequence Hub Data Security, 16 March 2016, pages 1-4). (Herein referred to as Bio-IT and BaseSpace, respectively.)
Bio-IT teaches a “highly reconfigurable DRAGEN Bio-IT Processor, which is integrated on a Field Programmable Gate Array (FPGA) card and is available in a preconfigured server that can be seamlessly integrated into bioinformatics workflows.” (Page 1, paragraph 4) Bio-IT further teaches “[t]he DRAGEN system is preconfigured with at least one fast file system consisting of a set of fast SSD disks…” (Page 22, paragraph 2) Additionally, Bio-IT teaches “variant calling, the pipeline supports calling of copy number and structural variants” (Page 2, paragraph 4) In addition, Bio-IT teaches “ultra rapid analysis of NGS data to identify cancer-associated mutations” (Page 95, lines 29-30) Bio-IT also teaches “DRAGEN can read directly from BCL [Binary Base Call] for map-align operations.” (pages 57, line 29) Bio-IT further teaches sequential workflow pipelines in Figures 1, 2, 3, and 11. (Pages 2, 62, 120, and 146) Bio-IT additionally teaches diagnostic workflows as “Somatic workflows [that] specify both tumor and normal inputs.” (Page 44, line 7) Bio-IT teaches “[t]o stream input files, you must have permission to access the remote files. The S3 object requires AWS authentication and credentials.” (page 59, lines 23-24) Bio-IT further teaches “[c]ommunication to the Illumina server is secured by encryption.” (Page 264: paragraph 6)
Bio-IT does not teach limited access to the shared network server, workflow containers, container orchestration, and scheduling the containers in series.
BaseSpace teaches “User-level authentication and inflight data encryption are enforced for every app that requests access to BaseSpace data.” (Page 1, right column, lines 3-4) BaseSpace further teaches “the run is authenticated against and tracked to a user-specific BaseSpace / MyIllumina account” and “sequencer software does not maintain any hosting/IIS services and does not carry a publicly addressable IP.” (Page 1, right column, lines 23-25 and Figure 2) Additionally, BaseSpace teaches “[t]he data stream is fully encrypted to the BaseSpace Hub.” (Page 2, Figure 4) BaseSpace teaches “projects are simple containers that store samples and AppResults.” (Page 1, right column, line 10 and left column, Figure 1) BaseSpace further teaches “[t]he BaseSpace Hub architecture stack consists of Amazon Web Services (AWS) Infrastructure-as-a Service (IaaS), the BaseSpace Platform-as-a-Service (PaaS), and Software-as-a Service (SaaS) components.” AWS provides container orchestration that can schedule containers sequentially. (Running Airflow on AWS Fargate, 20 January 2021, pages 1-9)
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to have combined the systems and methods of Illumina described in Bio-IT and in BaseSpace. All the features outlined in claims 1, 8, and 15 of the instant application were in use more than a year before the effective filing date, as indicated in the above cited evidence. Though this evidence is enumerated in different documents, the details applied to the same device already in use more than one year before the effective filing date. The invention is therefore prima facie obvious.
Claims 2 and 17 are rejected under 35 U.S.C. 103 as being unpatentable over Bio-IT and BaseSpace as applied to claims 1 and 15 above, and further in view of BaseSpace.
Bio-IT does not explicitly disclose “to implement the external sequencing diagnostic workflow identified from an external application hosted on the external server separate from the shared network server of the variant analysis model and the container orchestration engine” or “to execute the external sequencing diagnostic workflow generated by an external system on a server separate from the shared network server of the container orchestration engine and the variant analysis model.”
BaseSpace teaches BCL files in a subnetwork that is separate from the shared AWS network. (Page 2, Figure 4)
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to have combined the systems and methods of Illumina described in Bio-IT and in BaseSpace. All the features outlined in claims 1, 2, 15, and 17 of the instant application were in use more than a year before the effective filing date, as indicated in the above cited evidence. Though this evidence is enumerated in different documents, the details applied to the same device already in use more than one year before the effective filing date. The invention is therefore prima facie obvious.
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Bio-IT and BaseSpace as applied to claim 1 above, and further in view of Bio-IT and BaseSpace.
Every page of both Bio-IT and BaseSpace includes the statement: “For Research Use Only. Not for use in diagnostic procedures.” The specification of the instant application discloses “standardized genetic diagnostic protocols such as IVD or to comply with other analysis protocols such as IUO or RUO [Research Use Only].” [0061] Additionally, Bio-IT teaches using both WGS analysis and WES analysis (CNV Caller Options table, page 294, 1st and 6th rows). As stated in Alfares et al, “Whole-exome sequencing (WES) and whole-genome sequencing (WGS) are used to diagnose genetic and inherited disorders.” (Genetics in Medicine, 22 March 2018, pages 1328-1333) (Page 1328, “Purpose” section, line 1) Bio-IT states the communication to the server is secured by encryption (page 264: paragraph 6) and permission is needed to access remote files. (Page 41: paragraph 4 and page 59: paragraph 5)
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to have combined the systems and methods of Illumina described in Bio-IT and in BaseSpace. Although Bio-IT does not specifically indicate “grant, for a client device, access only to diagnostic applications compatible with the diagnostic execution mode,” it would have been obvious to apply known secure procedures to all aspects of the system. Given the known concerns about privacy regarding medical diagnostic data, one of ordinary skill in the art would have been motivated to incorporate security measures at all stages of the diagnostic process. As stated in BaseSpace, “Data security is a key concern in making the decision to move to cloud-based genomic storage and analysis.” (Page 1, left column, paragraph 2) The invention is therefore prima facie obvious.
Claims 4 and 13 are rejected under 35 U.S.C. 103 as being unpatentable over Bio-IT and BaseSpace as applied to claims 1 and 8 above, and further in view of Amazon Web Services: Overview of Security Processes. (Amazon Web Services, Amazon Web Services: Overview of Security Processes, May 2011) (Herein referred to as Overview.)
Bio-IT and BaseSpace do not directly disclose “to prevent the external sequencing diagnostic workflow from accessing sequencing data associated with the nucleotide base calls by applying read-only permissions to a workflow container that accesses the sequencing data and that is utilized by the external sequencing diagnostic workflow.”
It was stated in BaseSpace that Illumina is utilizing Amazon Web Services and their incorporated security features. BaseSpace references the document “Overview” in the “AWS Security Standards” section. Overview teaches “[a]n authenticated user can read an object only if the user has been granted Read permissions in an Access Control List.” (Page 16, paragraph 1, line 8) The Access Control List is used to manage permissions for S3 buckets, the Amazon Web Services containers.
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to have utilized the security features of Amazon Web Services to limit access to containers, specifically to apply read-only permissions to a workflow container that accesses sequencing data. As disclosed in BaseSpace, security for the Sequence Hub is coordinated through Amazon Web Services. Given the known concerns about privacy regarding sequencing data used for medical diagnostics, one of ordinary skill in the art would have been motivated to incorporate security measures at all stages of the process. As stated in BaseSpace, “Data security is a key concern in making the decision to move to cloud-based genomic storage and analysis.” (Page 1, left column, paragraph 2) The invention is therefore prima facie obvious.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Bio-IT and BaseSpace as applied to claim 1 above, and further in view of Overview.
Bio-IT and BaseSpace do not explicitly teach “to selectively prevent the one or more workflow containers from accessing sequencing data of the sample nucleotide sequence while executing the external sequencing diagnostic workflow.”
As indicated above, BaseSpace Sequence Hub is utilizing Amazon Web Services and BaseSpace references the document “Overview” in the “AWS Security Standards” section. Overview teaches “Amazon S3 APIs provide both bucket- and object-level access controls, with defaults that only permit authenticated access by the bucket and/or object creator.” (Page 16 paragraph 1, lines 4-5) Overview further teaches “Bucket and object level ACLs are independent; an object does not inherit ACLs from its bucket. Permissions to read or modify the bucket or object ACLs are themselves controlled by ACLs that default to creator-only access.” (Page 1, paragraph 1, lines 11-12)
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to have utilized the security features of Amazon Web Services to limit access to and by containers, specifically to prevent containers from accessing sequencing data. As disclosed in BaseSpace, security for the Sequence Hub is coordinated through Amazon Web Services. Given the known concerns about privacy regarding sequencing data used for medical diagnostics, one of ordinary skill in the art would have been motivated to incorporate security measures at all stages of the process. As stated in BaseSpace, “Data security is a key concern in making the decision to move to cloud-based genomic storage and analysis.” (Page 1, left column, paragraph 2) The invention is therefore prima facie obvious.
Claims 6 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Bio-IT and BaseSpace as applied to claims 1 and 15 above, and further in view of Overview.
Bio-IT and BaseSpace do not directly disclose to “isolate the one or more workflow containers by utilizing the targeted security permissions to individually designate sequencing data access permissions for the one or more workflow containers” or “to isolate the one or more workflow containers by preventing a workflow container of the one or more workflow containers from accessing sequencing data of the sample nucleotide sequence.”
As indicated above, BaseSpace Sequence Hub is utilizing Amazon Web Services and BaseSpace references the document “Overview” in the “AWS Security Standards” section. Overview teaches “Amazon S3 APIs provide both bucket- and object-level access controls.” (Page 16 paragraph 1, lines 4-5) Overview further teaches “[p]ermissions to read or modify the bucket or object ACLs are themselves controlled by ACLs that default to creator-only access. Therefore, the customer maintains full control over who has access to their data. Customers can grant access to their Amazon S3 data to other AWS Accounts.” (Page 1, paragraph 1, lines 11-14)
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to have utilized the security features of Amazon Web Services to limit access to and by containers, specifically to control accessing sequencing data by containers. As disclosed in BaseSpace, security for the Sequence Hub is coordinated through Amazon Web Services. Given the known concerns about privacy regarding sequencing data used for medical diagnostics, one of ordinary skill in the art would have been motivated to incorporate security measures at all stages of the process. As stated in BaseSpace, “Data security is a key concern in making the decision to move to cloud-based genomic storage and analysis.” (Page 1, left column, paragraph 2) The invention is therefore prima facie obvious.
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Bio-IT and BaseSpace as applied to claim 1 above, and further in view of Broad Communications. (Broad Institute, Illumina and Broad Institute announce agreement to co-develop genomic secondary analysis tools, 30 September 2019, pages 1-3) (Herein referred to as Broad.)
Bio-IT and BaseSpace do not explicitly teach “to receive the external sequencing diagnostic workflow generated by an external device operated by an external entity. “to receive the external sequencing diagnostic workflow generated by an external device operated by an external entity.” Although Bio-IT discloses inputting files in cBCL, FASTQ, BAM, CRAM, and GVCF formats, it does not indicate the specific sources of any of these files. (Page 2)
Broad teaches analyzing GATK files through the Illumina DRAGEN Bio-IT platform. Broad discloses “[t]he Broad Institute’s GATK is an industry leader for identifying SNPs and indels in germline DNA and RNA sequencing data. These tools were primarily designed to process exomes and whole genomes generated with Illumina sequencing technology. Over time, the scope expanded to include somatic short variant calling, and to tackle copy number variation (CNV) and structural variation (SV). In addition to variant callers, GATK also includes utilities to perform related tasks such as processing and quality control of high-throughput sequencing data.” (Page 2, paragraph 4) Broad further discloses “[t]he Illumina DRAGEN Bio-IT Platform delivers accurate, rapid secondary analysis for germline and somatic SNV, SV, CNV(A) calling as well as methylation, RNA and repeat expansion workflows. DRAGEN pipelines are hardware-accelerated using reconfigurable field-programmable gate array technology (FPGA). DRAGEN Pipelines can be deployed on-premise via a local server and in the cloud through Illumina’s BaseSpace Sequence Hub.” (Page 2, paragraph 5)
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to permit the system to receive external sequencing diagnostic workflows generated by an external device operated by an external entity. Permitting the DRAGEN platform to analyze sequencing data from outside sources would be obvious to try to expand the accessibility of the platform and its resources. As stated in Broad, “The co-developed secondary analysis software will provide a standardized methodology for processing high-throughput sequencing data and performing variant discovery analysis aiming for best-in-class sensitivity, accuracy and scalability. ‘This approach is a positive step for the community and will add to the available choices in data analysis to increase the quality and lower the cost of the current set of analysis methods,’ said Ewan Birney, Director, Global Alliance for Genomics and Health (GA4GH) and EMBL’s European Bioinformatics Institute. ‘The scientific community is well-positioned to benefit from this collaboration toward gold standard analysis methods and file formats which we believe will further enable inter-institution interoperability, research, and insights to maximize the impact of genomics in healthcare.’” (Page 2: paragraph 6, page 7: paragraph 1)
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Bio-IT and BaseSpace as applied to claim 8 above, and further in view of Overview.
Bio-IT and BaseSpace do not explicitly teach “isolating the one or more workflow containers comprises controlling access to different workflow data sources for the one or more workflow containers to prevent access to sequencing data by the external sequencing diagnostic workflow.”
As indicated above, BaseSpace Sequence Hub is utilizing Amazon Web Services and BaseSpace references the document “Overview” in the “AWS Security Standards” section. Overview teaches “Amazon S3 APIs provide both bucket- and object-level access controls, with defaults that only permit authenticated access by the bucket and/or object creator.” (Page 16 paragraph 1, lines 4-5) Overview further teaches “Bucket and object level ACLs are independent; an object does not inherit ACLs from its bucket. Permissions to read or modify the bucket or object ACLs are themselves controlled by ACLs that default to creator-only access.” (Page 1, paragraph 1, lines 11-12)
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to have utilized the security features of Amazon Web Services to limit access to and by containers, specifically to prevent containers from accessing sequencing data. As disclosed in BaseSpace, security for the Sequence Hub is coordinated through Amazon Web Services. Given the known concerns about privacy regarding sequencing data used for medical diagnostics, one of ordinary skill in the art would have been motivated to incorporate security measures at all stages of the process. As stated in BaseSpace, “Data security is a key concern in making the decision to move to cloud-based genomic storage and analysis.” (Page 1, left column, paragraph 2) The invention is therefore prima facie obvious.
Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Bio-IT and BaseSpace as applied to claim 8 above, and further in view of Bio-IT and Illumina Support: DRAGEN Germline Pipeline Online Help webpages. (Illumina Support, BaseSpace: DRAGEN Germline Pipeline Online Help, 2017, Analysis Output: Output Files, Pages 1-6) (Herein referred to as Output.)
BaseSpace does not teach “receiving an indication of a label defining a version of the variant analysis model and a memory allocation to utilize for executing the external sequencing diagnostic workflow.”
Bio-IT teaches a variety of variant call and variant analysis options, but does not specifically delineate the labeling options. Output discloses listings of output files each sample analysis in the DRAGEN Germline Pipeline, including specifically the BAM, VCF, and Genome VCF file formats. (Pages 1-6) Bio-IT discloses that a user “can load the reference genome and hash tables to DRAGEN card memory separately from processing reads.” (Page 49, lines 11-12) Bio-IT further discloses needed and available memory for DRAGEN Software, Size, and Seed Options. (Pages 18-20)
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to have provided specific labels to indicate variant analysis methods and to allocate sufficient memory to a diagnostic workflow. All the features outlined in claims 10 of the instant application were in use more than a year before the effective filing date, as indicated in the above cited evidence. Though this evidence is enumerated in different documents, the details applied to the same device already in use more than one year before the effective filing date. The invention is therefore prima facie obvious.
Claim 11 is rejected under 35 U.S.C. 103 as being unpatentable over Bio-IT and BaseSpace as applied to claim 8 above, and further in view of Bio-IT, BaseSpace, and AWS Illumina Solution Brief Security Compliance. (AWS and Illumina, Solution Brief: Security Compliance, 5 April 2019, Pages 1-2) (Herein referred to as Brief.)
BaseSpace does not explicitly disclose “designating a plurality of workflow data sources storing different types of workflow data; and activating, for a workflow container from among the one or more workflow containers, access to a first workflow data source of the plurality of workflow data sources while preventing access to other workflow data sources of the plurality of workflow data sources.”
Bio-IT teaches recommendations for input and output file storage locations (page 22) and references to file storage options and notations. (Pages 122, 155, 239, 250, 273, and 274) Brief teaches data sources and storage through Customer data, applications, and networks and AWS storage, database, and networks. (Page 1, AWS Shared Responsibility Model Diagram) Brief further teaches Granular Identity and Access Controls that regulate traffic flow with access control lists and isolated workloads run in Virtual Private Clouds. (Page 2, Key Security and Compliance Capabilities, middle column) Additionally, as referenced above, BaseSpace teaches the use of containers and an AWS container orchestration engine.
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to have utilized all the Illumina DRAGEN Bio-IT, BaseSpace Sequence Hub, and Amazon Web Service features to designate and differentiate workflow data sources and coordinate controlled access to workflow containers to limit access to workflow data sources. In addition to the above-mentioned rationale regarding security needs, one of ordinary skill in the art would have been motivated before the effective filing date to combine all the available features to provide privacy controls, sharing and collaboration, leveraging public and private tools, and advanced automation and integration. (Brief, page 1, BaseSpace Sequence Hub on AWS section) The invention is therefore prima facie obvious.
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over Bio-IT and BaseSpace as applied to claim 8 above, and further in view of Overview.
Bio-IT and BaseSpace do not directly disclose “mounting a plurality of workflow data sources as read only for the one or more workflow containers.”
It was stated in BaseSpace that Illumina is utilizing Amazon Web Services and their incorporated security features. BaseSpace references the document “Overview” in the “AWS Security Standards” section. Overview teaches “[a]n authenticated user can read an object only if the user has been granted Read permissions in an Access Control List.” (Page 16, paragraph 1, line 8) The Access Control List is used to manage permissions for S3 buckets, the Amazon Web Services containers.
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to have utilized the security features of Amazon Web Services to limit access to workflow data, specifically to apply read-only permissions to a workflow container. As disclosed in BaseSpace, security for the Sequence Hub is coordinated through Amazon Web Services. Given the known concerns about privacy regarding sequencing data used for medical diagnostics, one of ordinary skill in the art would have been motivated to incorporate security measures at all stages of the process. As stated in BaseSpace, “Data security is a key concern in making the decision to move to cloud-based genomic storage and analysis.” (Page 1, left column, paragraph 2) The invention is therefore prima facie obvious.
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Bio-IT and BaseSpace as applied to claim 8 above, and further in view Bio-IT and BaseSpace.
Although Bio-IT and BaseSpace do not explicitly teach “executing the external sequencing diagnostic workflow during a variant analysis by the variant analysis model,” they both reference the overarching concept.
Bio-IT teaches DRAGEN DNA Pipeline and DRAGEN RNA Pipeline which delineate the process of variant analysis through variant analysis models. (Page 2: Figure 1 and page 3: Figure 2) These figures clearly include the incorporation of sequencing data. BaseSpace teaches BCL files in a subnetwork that is separate from the shared AWS network. (Page 2, Figure 4)
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to have combined the systems and methods of Illumina described in Bio-IT and in BaseSpace. All the features outlined in claims 8 and 14 of the instant application were in use more than a year before the effective filing date, as indicated in the above cited evidence. Though this evidence is enumerated in different documents, the details applied to the same device already in use more than one year before the effective filing date. The invention is therefore prima facie obvious.
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Bio-IT and BaseSpace as applied to claim 15 above, and further in view of Bio-IT, BaseSpace and Overview.
Bio-IT and BaseSpace do not explicitly teach “to satisfy one or more standardized genetic diagnostic protocols while also executing the external sequencing diagnostic workflow by encoding a workflow execution application to grant the external sequencing diagnostic workflow read-only access to sequencing data associated with the nucleotide base calls of the sample nucleotide sequence during execution of the external sequencing diagnostic workflow.”
As referenced above, both Bio-IT and BaseSpace include the statement: “For Research Use Only. Not for use in diagnostic procedures.” In addition, as referenced above, Bio-IT teaches using both WGS analysis and WES analysis (CNV Caller Options table, page 294, 1st and 6th rows). (See specification [0061] and Alfares et al [Purpose] as referenced above for definitions of “standardized genetic diagnostic protocols”.) As stated above, BaseSpace teaches BCL files in a subnetwork that is separate from the shared AWS network. (Page 2, Figure 4) As indicated above, BaseSpace through Overview teaches “[a]n authenticated user can read an object only if the user has been granted Read permissions in an Access Control List” and “Amazon S3 APIs provide both bucket- and object-level access controls.” (Page 16, paragraph 1: line 8 and lines 4-5)
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to have combined the systems and methods described in Bio-IT, BaseSpace, and Overview. All the features outlined in claims 15 and 16 of the instant application were in use more than a year before the effective filing date, as indicated in the above cited evidence. Though this evidence is enumerated in different documents, the details applied to the same device already in use more than one year before the effective filing date. Furthermore, given the known concerns about privacy regarding sequencing data used for medical diagnostics, one of ordinary skill in the art would have been motivated to incorporate security measures at all stages of the process. As stated in BaseSpace, “Data security is a key concern in making the decision to move to cloud-based genomic storage and analysis.” (Page 1, left column, paragraph 2) The invention is therefore prima facie obvious.
Claim 19 is rejected under 35 U.S.C. 103 as being unpatentable over Bio-IT and BaseSpace as applied to claim 18 above, and further in view of Illumina DRAGEN Bio-IT Platform. (Illumina: Prepare Library: Sequence; Analyze Data, 5 June 2019, pages 1-5) (Herein referred to as Platform.)
Although Bio-IT makes frequent references to a variety of directories, Bio-IT and BaseSpace does not teach “instructions that, when executed by the FPGA, cause the computing device to prevent the workflow container from accessing the sequencing data by preventing the workflow container from accessing one or more workflow data sources comprising an input directory, an output directory, and an application directory.”
Platform teaches “The DRAGEN Platform features a robust suite of secondary analysis pipelines (Table 1) that support genome, exome, and RNA analysis. Pipelines can accept input files or create output files as different stages of the pipeline (Figure 3).” (Page 2, right column, paragraph 1) Additionally, Platform teaches “DRAGEN’s suite of analysis pipelines are engineered to run on field-programmable gate array technology (FPGAs), offering hardware-accelerated implementations of genomic analysis algorithms, including BCL conversion, mapping and alignment, sorting, duplicate marking and haplotype variant calling.” (Page 1, left column, paragraph 5) Platform further teaches “DRAGEN on-premise relies on a local storage solution to collect and store NGS data. Once the raw sequencing data has been transferred from the sequencing instrument to the local storage via a local network connection, DRAGEN transfers data from storage into the DRAGEN Server to perform the selected workflow, and then writes the generated analysis output files back to the local storage solution. The DRAGEN Server uses a Linux based command line interface (CLI) that can be configured for single command launch or advanced command line.” (Page 4, left column, paragraph 2 and Figure 5) Platform also teaches “Tight instrument integration enables encrypted data flow directly from the instrument into BaseSpace Sequence Hub for analysis, storage, sharing and other forms of data management (Figure 6).” (Page 4, right column, paragraph 3) Additionally, Platform discloses “Encrypted data flow from instrument to BaseSpace Sequence Hub can be easily setup on instrument during setup or post-installation via the settings menu.” (Page 4, right column, Figure 7 caption) Platform additionally teaches “DRAGEN on-premise offers a command line interface which can be used for single-command launch with an easy-to-learn Linux based command line interface (CLI) or advanced command line.” (Page 3, right column, paragraph 2 and Figure 4)
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to have combined the systems and methods described in Bio-IT, BaseSpace, and Platform. All the features outlined in claims 15, 18, and 19 of the instant application were in use more than a year before the effective filing date, as indicated in the above cited evidence. Additionally, the data storage and security features disclosed in Platform are further supported by the security features available through the interconnected AWS and Linux integrations. As discussed earlier, AWS can provide restrictions to container access. It is known that Linux CLI can be utilized to encrypt a folder from being searched or indexed. (Linux.com: Trainings and Tutorials, 4 February 2017, page 1) As addressed above, given the known concerns about privacy regarding sequencing data used for medical diagnostics, one of ordinary skill in the art would have been motivated to incorporate security measures at all stages of the process. The invention is therefore prima facie obvious.
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Bio-IT and BaseSpace as applied to claim 15 above, and further in view of Illumina BaseSpace Sequence Hub Help Center Biosample Workflow Files and Automation Overview webpages. (Illumina Support, BaseSpace: Sequence Hub Help Center, Automation Overview, 8 December 2018, page 1 and Analysis Workflows, 8 December 2018, page 1) (Herein referred to as Automation and Workflow, respectively.)
Bio-IT and BaseSpace do not teach to “cause the computing device to trigger execution of the external sequencing diagnostic workflow by receiving, via the container orchestration engine, a post defining parameters for implementing the external sequencing diagnostic workflow.”
Automation teaches “features to support automating data analysis and management, “ including “[s]chedule apps to automatically launch after required data or other dependencies have been met.” (Page 1, intro and 5th bullet) Workflow teaches “[a]nalysis workflows are packaged templates of BaseSpace Sequence Hub Apps with predefined settings and QC thresholds to support automation of running analyses. Use an analysis workflow to automatically launch the same app configurations on different biosamples in the project.” (Page 1, paragraph 1)
It would have been prima facie obvious to one of ordinary skill in the art at the effective
filing date of the invention to have provided a mechanism to trigger the execution of a sequencing diagnostic workflow coordinated by the BaseSpace Sequence Hub. All the features outlined in claims 15 and 20 of the instant application were in use more than a year before the effective filing date, as indicated in the above cited evidence. Though this evidence is enumerated in different documents, the details applied to the same device already in use more than one year before the effective filing date. The invention is therefore prima facie obvious.
Conclusion
Claims 1-20 are eligible under 35 USC 101 (eligibility) because programming the FPGA to schedule and execute the workflow in containers is a particular machine (Step 2A: Prong 2).
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. AWS Genomics Guide teaches common strategies and best practices used successfully by Amazon Web Services (AWS) customers for analyzing genomics sequencing data. (AWS, August 2017, pages 1-34) Gao et al teaches using a Field Programmable Gate Array (FPGA), a computer readable storage medium, and local and cloud servers, nucleotide base calls, variant calling, using containers, a diagnostics mode, a secure connection, encryption for secure delivery, and a separate analysis pipeline and workflow engine with an internal server. (US 2021/0057090 A1) Mathur et al teaches security components to restrict access, sequential algorithm execution, a remote server, use of containers, an FPGA, computer readable media, diagnosis model algorithms, and algorithm orchestration integrated into workflows through external sources. (US 2021/10174941 A1)
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SHARON LEVINE GRAFF whose telephone number is (571)317-0219. The examiner can normally be reached Mon - Fri 7:30 AM - 4 PM.
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, Karlheinz Skowronek can be reached at (571) 272-9047. 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.
/S.L.G./ Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
Prosecution Insights