CN-121986282-A - DNA sequencing system and use thereof

Abstract

The present disclosure provides flow cell devices, systems, and methods for facilitating and performing DNA sequencing analysis with reduced system complexity and cost, significant cost savings, and reduced contamination levels. The sequencing system described herein allows for multiple flow cells to be processed simultaneously such that sequencing steps and imaging steps or multiple sequencing methods can be performed in parallel using a single sequencing system.

Inventors

• D. Hastings
• D fuller
• M. prevett
• J. Nismith
• C. Niman
• B.Xie
• R. Hudima
• A. Gomez
• J. Lipschel
• T. ZIEGLER
• J.Ye
• M. DeAngelo
• XING SIYUAN

Assignees

• 元素生物科学公司

Dates

Publication Date

20260505

Application Date

20240725

Priority Date

20230726

Claims (20)

1. 1. A sequencing system, comprising: An optical system 2020 including an objective lens; An x-y stage 2010 configured to hold a sample to be imaged thereon and to move the sample relative to the objective lens in an x-y plane, wherein the sample is fixed on one or more flow cell devices; A nested set 2050 configured to provide fluid and thermal communication to the sample when the one or more flow cell devices are coupled to the nested set, and A movement mechanism 2040, optionally comprising a movable arm configured to move the one or more flow cell devices between the x-y stage 2010 and nested set 2050 during sequential operation.
2. 2. The sequencing system of claim 1, wherein the x-y stage 2010 is automatically actuated by a first actuator with a first spatial precision.
3. 3. The sequencing system of claim 1 or 2, wherein the movable arm is automatically actuated by a second actuator with a second spatial precision.
4. 4. The sequencing system of any of the preceding claims, wherein the first actuator, the second actuator, or both are controlled by one or more hardware processors of the sequencing system.
5. 5. The sequencing system of any of the preceding claims, wherein the sequencing system further comprises: a housing configured to retain one or more of the optical system 2020, the x-y stage 2010, the nested set 2050, and the movement mechanism 2040 within the housing.
6. 6. The sequencing system of any of the preceding claims, wherein the movable arm is automatically actuated to move in three dimensions (3D).
7. 7. The sequencing system of any of the preceding claims, wherein movement in each of the three dimensions occurs with one or more predetermined spatial accuracies.
8. 8. The sequencing system of any of the preceding claims, wherein the sequencing system lacks fluid or thermal communication with the one or more flow cell devices at or near the x-y stage 2010 when the flow cell devices are affixed to the x-y stage 2010.
9. 9. The sequencing system of any of the preceding claims, wherein each of the one or more flow cell devices comprises an open landing area configured to openly receive fluid from the nested group 2050.
10. 10. The sequencing system of any of the preceding claims, wherein the flow cell device comprises a plurality of microfluidic channels, and the nested set 2050 is configured to allow fluid communication with each of the plurality of microfluidic channels independently and simultaneously.
11. 11. The sequencing system of any of the preceding claims, wherein the flow cell device comprises a plurality of microfluidic channels, and the nested set 2050 is configured to allow independent and sequential fluid communication with each of the plurality of microfluidic channels.
12. 12. The sequencing system of any of the preceding claims, wherein the flow cell device comprises a plurality of microfluidic channels, and the nested set 2050 is configured to allow fluid communication with each of the plurality of microfluidic channels independently and without cross-contamination.
13. 13. The sequencing system of any of the preceding claims, wherein the x-y stage 2010 is actuated to move a predetermined distance within the x-y plane.
14. 14. The sequencing system of any of the preceding claims, wherein the predetermined distance is based on a distance between two adjacent microfluidic channels of the flow cell device.
15. 15. The sequencing system of any of the preceding claims, wherein the nested set 2050 is configured to enable fluid and thermal communication with the one or more flow cell devices.
16. 16. The sequencing system of any of the preceding claims, wherein the nested set 2050 is configured to enable fluid and thermal communication with at least 1, 2,3, 4, 5, 6, 7, 8, 9, or 10 flow cell devices when each of the flow cell devices is in a locked position with the nested set 2050.
17. 17. The sequencing system of any of the preceding claims, wherein the nested set 2050 is configured to hold each of the flow cell devices in an unlocked position in which the flow cell devices are removable from the nested set 2050 and a locked position in which the flow cell devices are spatially registered to the nested set 2050, fixedly coupled to the nested set 2050, and capable of sealed fluid and thermal communication between the nested set and the flow cell devices.
18. 18. The sequencing system of any of the preceding claims, wherein the flow cell device is coupled to a carrier 2051.
19. 19. The sequencing system of any of the preceding claims, wherein the movable arm is configured to move the carrier 2051 and the flow cell device together.
20. 20. The sequencing system of any of the preceding claims, wherein the carrier 2051 is configured to spatially register to the nested set in the locked position.

Description

DNA sequencing system and use thereof Cross Reference to Related Applications The present application claims priority and benefit from U.S. provisional application Ser. Nos. 63/515,816 and 63/666,463, filed on 7.26 of 2023, and 7.1 of 2024, the contents of each of which are incorporated herein by reference in their entirety. Background In a New Generation Sequencing (NGS) system, a flow cell device is used to immobilize template nucleic acid molecules derived from a biological sample, and then a repeated flow of sequencing reagents is introduced to attach labeled nucleotides to specific positions in the template sequence. A series of signals from the labels are detected and decoded to reveal the nucleotide sequence of the corresponding template molecule, e.g., an immobilized and/or amplified nucleic acid template molecule attached to the surface of the flow cell. Typical NGS systems allow for fluid and thermal communication from the system to the flow cell device and sample immobilized thereon during sequencing while the sample remains in a fixed position relative to the sequencing system optics. However, placing the flow cell in a fixed position relative to the sequencing system optics during steps that do not involve imaging can result in inefficient use of the optical system and reduce the efficiency of the NGS system. Thus, there is a need in the art for compositions, systems, and methods that allow for asynchronous processing of multiple samples or portions of samples in parallel. Using the compositions, systems, and methods of the present disclosure, imaging and non-imaging steps for different samples may occur simultaneously, or different samples may undergo different methods simultaneously, thereby reducing idle time, increasing flexibility, and increasing efficiency. Disclosure of Invention Described herein are sequencing systems for sequencing nucleic acids that have flexibility and scalability. The sequencing systems and methods described herein may advantageously enable more efficient use of an optical system with minimal idle time (e.g., waiting for fluid administration). The systems and methods herein may advantageously allow for imaging of a sample while sequencing reactions in another sample occur in parallel, thereby improving throughput of existing sequencing systems. The systems and methods described herein may advantageously separate the sample being imaged from fluid and/or thermal communication, thereby simplifying system architecture and enabling more compact dimensions than existing systems. The systems and methods described herein may also advantageously enable independent fluid and/or thermal communication with various samples, thereby allowing a user to image samples using different reagents or sequencing protocols and potentially combine them within a single sequence run. The present disclosure provides a sequencing system comprising an optical system 2020 comprising an objective lens, an x-y stage 2010 configured to hold a sample to be imaged thereon and to move the sample relative to the objective lens in an x-y plane, wherein the sample is fixed on one or more flow cell devices, a nested set 2050 configured to provide fluid and thermal communication to the sample when the one or more flow cell devices are coupled to the nested set, and a movement mechanism 2040 optionally comprising a movable arm configured to move the one or more flow cell devices between the x-y stage 2010 and the nested set 2050 during a sequence operation. In some embodiments, the x-y stage 2010 is automatically actuated by a first actuator with a first spatial accuracy. In some embodiments, the movable arm is automatically actuated by a second actuator with a second spatial precision. In some embodiments, the first actuator, the second actuator, or both are controlled by one or more hardware processors of the sequencing system. In some embodiments, the sequencing system further includes a housing configured to retain one or more of the optical system 2020, the x-y stage 2010, the nested set 2050, and the movement mechanism 2040 within the housing. In some embodiments, the movable arm is automatically actuated to move in three dimensions (3D). In some embodiments, movement in each of the three dimensions occurs with one or more predetermined spatial accuracies. In some embodiments, when the flow cell devices are fixed on the x-y stage 2010, the sequencing system lacks fluid or thermal communication with one or more flow cell devices at or near the x-y stage 2010. In some embodiments, each of the one or more flow cell devices includes an open landing area configured to openly receive fluid from the nested group 2050. In some embodiments, the flow cell device comprises a plurality of microfluidic channels, and the nested group 2050 is configured to allow independent and simultaneous fluid communication with each of the plurality of microfluidic channels. In some embodiments, the flow cell device comprises a