JP-7857215-B2 - Method for controlling sequencing devices

JP7857215B2JP 7857215 B2JP7857215 B2JP 7857215B2JP-7857215-B2

Inventors

ガオ，ジン
クドリンガー，ヴィドヤ
ライ，ディレンダラクマール

Assignees

ライフテクノロジーズコーポレーション

Dates

Publication Date: 20260512
Application Date: 20200731
Priority Date: 20200529

Claims (20)

The local server system receives an assay definition file from a server in a cloud computing and storage system, wherein the assay definition file includes code modules for constructing the assay, and the code modules constitute steps in the workflow for the assay, including library preparation, templating, sequencing, and analysis pipelines . The code module is stored in the memory of the local server system, The local server system receives sequencing data from a sequencing device, wherein the sequencing data is generated by the sequencing device during sequencing execution according to an instrument script from the assay definition file for the assay. Applying an analytical pipeline for the assay to the sequencing data, wherein the analytical pipeline includes analytical steps performed by the processor of the local server system according to the code module from the assay definition file to generate assay analysis results, method.
The method according to claim 1, wherein the code module for the analysis pipeline includes a code module for a base calling step, and the base calling step generates a sequence read.
The method according to claim 2, wherein the code module for the analysis pipeline includes a code module for an alignment step, and the alignment step generates an aligned sequence read.
The method according to claim 3, wherein the code module for the analysis pipeline includes a code module for a variant calling step, the variant calling step being applied to the aligned sequence readout to generate a variant calling result.
The method according to claim 4, further comprising storing the variant calling results in the variome database of the local server system.
The method according to claim 1, further comprising displaying the assay analysis results, wherein the display includes an image file for presenting the results for the assay.
The method according to claim 6, wherein the assay definition file includes the image file for presenting the results for the assay.
The method according to claim 1, wherein the assay definition file includes a reference genome file.
The method according to claim 1, wherein the assay definition file includes a list of annotation sources.
The method according to claim 1, wherein the analysis pipeline is applied in parallel to the sequencing data corresponding to multiple lanes of a sequencing chip installed in the sequencing device.
The method according to claim 10, wherein each of the plurality of lanes corresponds to a respective assay, and the step of applying the analysis pipeline is to apply the analysis step of each assay to the sequencing data for the lane.
The method according to claim 1, further comprising displaying a page to the user on the user interface of the local server system for selecting the assay definition file to import from the cloud computing and storage system to the local server system.
The method according to claim 1, further comprising a plurality of assay definition files, wherein the plurality of assay definition files include a research use only (RUO) mode assay definition file and an in vitro diagnostic (IVD) mode assay definition file.
It is a local server system, Memory and A processor, which, when executed by the processor, on the local server system, The local server system receives an assay definition file from a server of the cloud computing and storage system, wherein the assay definition file includes code modules for configuring the assay, and the code modules constitute steps in the workflow for the assay, including library preparation, templating, sequencing, and analysis pipelines . The code module is stored in the memory of the local server system, The local server system receives sequencing data from a sequencing device, wherein the sequencing data is generated by the sequencing device during sequencing execution according to an instrument script from the assay definition file for the assay. Applying an analytical pipeline for the assay to the sequencing data, wherein the analytical pipeline includes analytical steps performed by the processor of the local server system according to the code module from the assay definition file to generate assay analysis results, Configured to execute instructions that cause the method to be performed, Equipped with a processor, Local server system.
The local server system according to claim 14, wherein the code module for the analysis pipeline includes a code module for a base calling step, and the base calling step generates a sequence read.
The local server system according to claim 15, wherein the code module for the analysis pipeline includes a code module for an alignment step, and the alignment step generates an aligned sequence read.
The local server system according to claim 16, wherein the code module for the analysis pipeline includes a code module for a variant invocation step, the variant invocation step is applied to the aligned sequence reads to generate a variant invocation result.
The local server system according to claim 17, further comprising a variome database for storing the results of the variant calling.
The local server system according to claim 14, further comprising a plurality of assay definition files, wherein the plurality of assay definition files include a research use only (RUO) mode assay definition file and an in vitro diagnostic (IVD) mode assay definition file.
The local server system according to claim 14, further comprising a first database and a second database, the first database storing information for a research use-only (RUO) mode of the operation and the second database storing information for an in vitro diagnostic (IVD) mode of the operation.

Description

(Cross-reference of related applications) This application claims the benefits under Section 119(e) of U.S. Patent Act, relating to U.S. Provisional Application No. 62/889,109, filed on 20 August 2019, and U.S. Provisional Application No. 62/704,806, filed on 29 May 2020. The entire contents of the aforementioned applications are incorporated herein by reference. This disclosure relates to the control of sequencing devices for next-generation sequencing (NGS), including the digital delivery of modular software components encompassing assay workflows from cloud-based computing and storage system resources. Biological and medical scientific research is increasingly relying on nucleic acid sequencing to enhance biological research and medicine. For example, biologists and zoologists are using sequencing to study animal migration, species evolution, and the origins of traits. The medical community is using sequencing to study the origins of diseases, drug susceptibility, and infections. Therefore, sequencing has broad applicability to virtually all aspects of biology, therapy, diagnosis, forensic medicine, and scientific research. Nevertheless, the use of sequencing can be limited by assay availability, sequencing run time, preparation time, and cost. Additionally, quality sequencing has historically been an expensive process, limiting its practice. Laboratory molecular pathology testing can be enhanced by a wide selection of assays developed for sequencing devices such as NGS sequencing devices. Server systems configured to control sequencing devices can implement a modular software platform supporting rapid expansion of molecular testing menus, enabling rapid laboratory adoption of assays. Assay content and corresponding workflows can be delivered as modular software components from cloud-based computing and storage system resources (e.g., Thermo Fisher Cloud, Thermo Fisher Scientific, Waltham, Massachusetts). Assay configurations and corresponding workflows are delivered to the user's server system as modular software components in an assay definition file (ADF). The assay definition file supports backward compatibility of workflow software modules and separation of workflow software modules from the server system's platform software. The server system and modular software components can be configured to control multiple functional modes, including a Research Use Only (RUO) or Assay Development (AD) mode, and an In Vitro Diagnostic (IVD) or Dx mode. The RUO or AD mode supports assay development and digital distribution for research applications and third-party development of assays (RUO and AD are used interchangeably). The IVD or Dx mode supports digital distribution of molecular diagnostic assays that meet local requirements for diagnostic applications (IVD and Dx are used interchangeably). Multiple functional modes allow the same NGS sequencing device to be used for both RUO and IVD assays. According to an exemplary embodiment, a method is provided comprising: receiving an assay definition file from a server of a cloud computing and storage system, wherein the assay definition file includes code modules for configuring the assay; storing the code modules in the memory of the local server system; receiving sequencing data from a sequencing device, wherein the local server system receives sequencing data generated by the sequencing device during sequencing execution for the assay; and applying an analysis pipeline for the assay to the sequencing data, wherein the analysis pipeline includes analysis steps executed by the processor of the local server system according to the code modules from the assay definition file to generate assay analysis results. According to an exemplary embodiment, a local server system is provided, comprising: a memory; and a processor, which, when executed by the processor, causes the local server system to perform a method including: receiving an assay definition file from a server of a cloud computing and storage system, wherein the assay definition file includes code modules for configuring the assay; storing the code modules in the memory of the local server system; receiving sequencing data from a sequencing device, wherein the sequencing data is generated by the sequencing device during sequencing execution for the assay; and applying an analysis pipeline for the assay to the sequencing data, wherein the analysis pipeline includes analysis steps performed by the processor of the local server system according to the code modules from the assay definition file to generate assay analysis results. Novel features are specifically revealed in the attached claims. A better understanding of the features and advantages will be obtained by referring to the following detailed description illustrating exemplary embodiments and attached drawings. A schematic diagram of the server system components according to the embodiment is shown.This is a block diagram of the analysis pipeline accord