Sequencing method, processing system and sequencing system

Abstract

A sequencing method, a data processing system and a gene sequencing system for a semiconductor sequencing chip, the semiconductor sequencing chip comprising a plurality of core rows formed by arranging a plurality of cores, the sequencing method comprising: controlling the semiconductor sequencing chip to immerse in a reagent used in each round of sequencing reaction in an immersion manner that the core rows are immersed in units, when the semiconductor sequencing chip is immersed into the substrate reagent, the corresponding basic group emits light or does not emit light; when at least one unit of core line is immersed into the substrate reagent, reading data output by the core line immersed into the reagent for at least one time until all the core lines are immersed into the substrate reagent, determining a signal range of whether the basic group is luminous or not limited by the target template by using the data output by the first core line, and simplifying the data output by the other core lines by using the target template to obtain optical signal data; and determining the type of the base according to the optical signal data.

Description

Sequencing methods, processing systems, sequencing systems Technical Field

[0001] The present invention relates to the field of gene sequencing technology, and in particular to a sequencing method, a data processing system and a gene sequencing system. Background Art

[0002] The sequencing substrates (also known as semiconductor sequencing chips) used in existing high-throughput gene sequencers are commonly divided into two types: surface-mount chips and semiconductor sequencing chip integrated circuits. The former typically captures fluorescence signals through a microscope optical system, while semiconductor sequencing chips use internal integrated circuits to collect and convert electrical or optical signals into analog-to-digital signals.

[0003] When sequencing using a semiconductor sequencing chip, the signals output by all pixels are read and processed to produce an image. Complex image processing algorithms are then used to cluster the scatter plot, thereby identifying the four different bases of ATCG. However, image processing algorithms consume a large amount of computing resources, and the computational load becomes increasingly unacceptable when generating high-throughput or even ultra-high-throughput data.

[0004] Summary of the Invention

[0005] The present invention aims to address at least one of the technical problems existing in the prior art. To this end, the present invention provides a sequencing method, a data processing system, and a gene sequencing system. The sequencing method is simple and can significantly reduce the amount of data processing, thereby significantly reducing the amount of data transmitted and processed by back-end servers.

[0006] An embodiment of the present invention provides a sequencing method for a gene sequencing system, wherein the semiconductor sequencing chip includes a plurality of cores arranged to form a plurality of core rows. The sequencing method includes:

[0007] Controlling the semiconductor sequencing chip to contact the reagents used in each round of sequencing reaction in a manner of core behavior contact units, so that the corresponding bases emit light or do not emit light based on the semiconductor sequencing chip contacting the reagents;

[0008] Based on each core row contacting N units in the reagent, N>0, read the data output by the core row contacting the reagent at least once until all core rows are contacted with the reagent,

[0009] wherein, after reading the data output by the first core row, determining the target template according to the data output by the first core row, wherein the target template includes a signal range indicating whether the base emits light;

[0010] Simplifying the data output by the remaining core rows according to the target template to obtain optical signal data of different bases;

[0011] The base type is determined based on the optical signal data.

[0012] The above sequencing method contacts the core rows in a contact manner using the core rows as contact units, and determines the target template based on the data output by the first core row, so as to simplify the data output by the remaining core rows to obtain optical signal data of different bases, which can greatly reduce the data processing volume of the remaining core rows, and thus greatly reduce the amount of data transmitted and processed.

[0013] An embodiment of the present invention provides a data processing system for a gene sequencing system. The data processing system includes a semiconductor sequencing chip, a control device, and a manipulator. The semiconductor sequencing chip includes a processing module and multiple cores, the multiple cores are arranged in an array to form multiple core rows, the processing module connects the core rows and the control device, and the control device is connected to the manipulator.

[0014] The control device is used to:

[0015] Controlling the manipulator to contact the semiconductor sequencing chip with a reagent used for a sequencing reaction in a manner of a core behavior contact unit, so that the corresponding base emits light or does not emit light based on the semiconductor sequencing chip contacting the reagent;

[0016] The processing module is used for:

[0017] Based on each contact of N units of the core row in the reagent, N>0, data output by the core row contacting the reagent is read at least once until all core rows are contacted with the reagent.

[0018] An embodiment of the present invention provides a gene sequencing system, including the above-mentioned data processing system.

[0019] The above-mentioned data processing system and gene sequencing system contact the core rows in a contact manner in which the core rows are contact units, and determine the target template based on the data output by the first core row, so as to simplify the data output by the remaining core rows to obtain optical signal data of different bases, which can greatly reduce the data processing volume of the remaining core rows, and thus greatly reduce the amount of data transmitted and processed.

[0020] Additional aspects and advantages of the present invention will be set forth in part in the description which follows and, in part, will be obvious from the description which follows, or may be learned by practice of the present invention. BRIEF DESCRIPTION OF THE DRAWINGS

[0021] The above and / or additional aspects and advantages of the present invention will become apparent and readily understood from the description of the embodiments with reference to the following drawings, in which:

[0022] FIG1 is a flow chart of a sequencing method according to an embodiment of the present invention;

[0023] FIG2 is a schematic diagram of a module of a data processing system of a semiconductor sequencing chip according to an embodiment of the present invention;

[0024] FIG3 is a schematic diagram of an image control module of a data processing system of a semiconductor sequencing chip according to an embodiment of the present invention;

[0025] FIG4 is a schematic diagram of a target template of a sequencing method according to an embodiment of the present invention;

[0026] FIG5 is a schematic diagram showing the correspondence between optical signal data and base types according to an embodiment of the present invention;

[0027] FIG6 is a schematic structural diagram of a semiconductor sequencing chip according to an embodiment of the present invention;

[0028] FIG7 is a schematic diagram of the area division of a semiconductor sequencing chip according to an embodiment of the present invention;

[0029] FIG8 is a schematic structural diagram of a semiconductor sequencing chip core according to an embodiment of the present invention;

[0030] FIG9 is another schematic structural diagram of a semiconductor sequencing chip core according to an embodiment of the present invention;

[0031] FIG10 is another schematic structural diagram of the semiconductor sequencing chip core according to an embodiment of the present invention;

[0032] FIG11 is a timing diagram of data reading according to an embodiment of the present invention;

[0033] Reference numerals:

[0034] Manipulator 10, target template 11, reagent tank 12, first signal range 13, semiconductor sequencing chip 14,

[0035] The second signal range 15, the mechanical control module 16, the third signal range 17, the fluid control module 18,

[0036] Fourth signal range 19, temperature control module 20, environment control module 22, image processing module 24,

[0037] Control device 26, display screen 28, control module 30, power board 32, row switching and common reading unit 34,

[0038] Main control board 36, driver board 40, core 42, core row 44, region 48, sub-pixel array 50,

[0039] Pixel array 51, phase-locked loop, decoder controller and digital buffer 52,

[0040] Correlated double sampling circuit and comparator 54, readout circuit 56, decoder and driver 58,

[0041] Data processing system 100. DETAILED DESCRIPTION

[0042] The following describes embodiments of the present invention in detail, examples of which are shown in the accompanying drawings, wherein the same or similar reference numerals throughout represent the same or similar elements or elements having the same or similar functions. The embodiments described below with reference to the accompanying drawings are exemplary and are intended to be used to explain the present invention, and are not to be construed as limiting the present invention.

[0043] 1 , 2 and 6 , an embodiment of the present invention provides a sequencing method for a semiconductor sequencing chip 14 for use in a gene sequencing system. The semiconductor sequencing chip 14 includes a plurality of cores 42 , which are arranged to form a plurality of core rows 44 .

[0044] Among them, the semiconductor sequencing chip 144 can include a sequencing surface and a back plate, or it can include two sequencing surfaces, the sequencing surface includes the core 42, and the back plate is a surface that does not include the core 42. The sequencing surface and the reagent can achieve the purpose of contact through the action of "contact", and the contact action can be achieved in several ways, but not limited to these: the reagent achieves the purpose of contact with the fixed sequencing surface by flowing, unfolding, etc.; the sequencing surface is immersed in the reagent by moving, rotating, etc. to achieve the purpose of contact; the sequencing surface and the reagent achieve the purpose of contact by relative motion. The above methods can all achieve the contact between the sequencing surface and the reagent, and it should be understood that they can be replaced according to the actual usage scenario. In order to facilitate the explanation of the essential content of the present disclosure, "the purpose of contact is achieved by immersing the sequencing surface in the reagent by moving" is used as an example for explanation.

[0045] Sequencing methods include:

[0046] Step 101: Control the semiconductor sequencing chip 14 to immerse it in reagents for each round of sequencing reaction, using core rows 44 as immersion units. The reagents include at least two substrate reagents. When the semiconductor sequencing chip 14 is immersed in the substrate reagents, the corresponding bases are caused to emit light or not emit light.

[0047] Step 103, when each time N units of core rows 44 are immersed in the substrate reagent (N>0), read the data output by the core rows 44 immersed in the reagent at least once until all core rows 44 are immersed in the substrate reagent.

[0048] After reading the data output by the first core row 44, the target template 11 is determined using the data output by the first core row 44. The target template 11 includes a signal range indicating whether the base emits light.

[0049] Step 105 , using the target template 11 to simplify the data output by the remaining core rows 44 to obtain optical signal data of different bases;

[0050] Step 107: Determine the base type based on the optical signal data.

[0051] In the above sequencing method, the semiconductor sequencing chip 14 is immersed in a manner of immersion with the core row 44 as the immersion unit, and the data output by the first core row 44 is used to determine the target template 11, so as to simplify the data output by the remaining core rows 44 to obtain optical signal data of different bases, which can greatly reduce the amount of data transmitted and processed.

[0052] The semiconductor sequencing chip 14 includes multiple cores 42 arranged to form multiple core rows 44. Initially, the core row 44, which is immersed in the reagent first, is loaded with base sequence clusters / balls obtained by amplifying different starting fragments through the same amplification process. In one example, the first core row 44 contains only one core 42, which is loaded with base sequence clusters / balls obtained by amplifying different starting fragments (e.g., insert sizes of 50 bp, 100 bp, 200 bp, and 300 bp) through the same amplification process. Through this process, the first core row 44 of the semiconductor sequencing chip 14 can produce a target template 11 after the biochemical reaction.

[0053] During the sequencing process, the semiconductor sequencing chip 14 is immersed in the reagents used for each round of sequencing reaction, with core rows 44 being the immersion unit. The reagents include at least two substrate reagents. When the semiconductor sequencing chip 14 is immersed in the substrate reagents, the substrate reagents cause different base types to exhibit different luminescence intensities. Every time N (N>0) core rows 44 are immersed in the substrate reagent, the optical signal data output by the core row 44 is read. The data output by the remaining core rows 44 is simplified using the target template 11 to obtain optical signal data of different bases. The base type can be determined based on the optical signal data output by the semiconductor sequencing chip 14.

[0054] The immersion unit for each immersion of the reagent is N, and the value of N represents the number of core rows 44 that enter the reagent each time. When N=1, each time a core row 44 is immersed, the data output by the semiconductor sequencing chip 14 is read once. N can be made a value greater than 1. At this time, each time N core rows 44 are immersed, the data output by the semiconductor sequencing chip 14 is read once to increase the speed of data reading. Or for compatible devices with slower reading speeds, N=0.5 can be made. At this time, one core row 44 is immersed and the data is read twice. The number of core rows 44 immersed in the reagent each time and the number of times the signal is read each time need to be set according to actual conditions and are not specifically limited here.

[0055] In one embodiment, the reagents include two substrate reagents. After the first core row 44 of the semiconductor sequencing chip 14 outputs data from the two substrate reagents (i.e., two channel data), a target template 11 is obtained. As shown in FIG4 , the target template 11 includes a signal range indicating whether a base emits light (such as the range defined by the dashed box in FIG4 ) and the data output by the remaining core rows 44 are simplified and processed to obtain optical signal data for different bases. The output optical signal data can be used to determine the type of the base.

[0056] Please refer to Figure 2. The data processing system 100 according to an embodiment of the present invention includes a semiconductor sequencing chip 14, a control device 26, and a manipulator 10. Reagents can be placed in a reagent tank 12. The manipulator 10, the reagent tank 12, and the semiconductor sequencing chip 14 can be placed in a closed space, and a series of biochemical reactions for gene sequencing are carried out in the closed space. There can be one or more reagent tanks 12, and each reagent tank 12 contains the reagents required for gene sequencing. The biochemical reactions occurring in the reagent tanks 12 need to maintain a certain temperature, time, and environment, and these conditions are controlled by the control device 26.

[0057] The semiconductor sequencing chip 14 includes a processing module (not shown) and multiple cores 42. The multiple cores 42 are arranged in an array to form multiple core rows 44. The processing module connects the core rows 44 and the control device 26. After each unit of the core row 44 is immersed in the substrate reagent, the processing module reads the data output by the core row 44, uses the data output by the first core row 44 to determine a target template 11, and uses the target template 11 to limit the signal range of whether the base is luminous. The target template 11 is used to simplify the data output by the remaining core rows 44 to obtain and output light signal data of different bases.

[0058] Control device 26 may include a display screen 28 and a control module 30. Display screen 28 may be a touch screen display, through which the operator controls the entire gene sequencing process. Control module 30 may include mechanical control module 16, fluid control module 18, temperature control module 20, environmental control module 22, and image processing module 24.

[0059] Among them, the mechanical control module 16 is used to control the movement of the manipulator 10 to clamp the semiconductor sequencing chip 14, and control the semiconductor sequencing chip 14 to immerse into the reagent in the reagent tank 12 in an immersion manner with the core row 44 as the immersion unit. The mechanical control module 16 can control the reaction time of the semiconductor sequencing chip 14 in the reagent tank 12. At the same time, the mechanical control module 16 can control the movement speed of the manipulator 10 within an appropriate value range, which can reduce the amount of reagent brought out by the semiconductor sequencing chip 14 when entering and exiting the reagent tank. At the same time, the appropriate movement speed of the manipulator 10 can also reduce the amount of bubbles generated in the reagent.

[0060] The fluid control module 18 is used to monitor the reagent content in the reagent tank 12. By detecting the quality of the reagent, the fluid control module 18 can monitor the changes in the reagent content in the reagent tank, and then is responsible for controlling the relevant water pumps and valves to replenish and circulate the reagent to keep the content of key reactants required for biochemical reactions in the reagent at a certain level.

[0061] The temperature control module 20 is used to monitor and control the temperature in the enclosed space through a temperature sensor to maintain it at a suitable temperature required for the biochemical reaction.

[0062] The environment control module 22 is used to monitor and control the content of various major gases in the closed space, and ensure that the biochemical reaction is carried out in a low-oxygen environment by filling nitrogen or other means.

[0063] Referring to Figure 3 , the image processing module 24 is connected to the semiconductor sequencing chip 14 via an interface board 38 . The image processing module 24 comprises a row switching and common reading unit 34 , a main control board 36 , and a driver board 40 . The row switching and common reading unit 34 reads the image signals collected by the semiconductor sequencing chip 14 row by row and transmits them to the backend hard drive for storage. The row switching and common reading unit 34 also communicates with the main control board 36 for bidirectional data transmission. The power board 32 supplies power to the image processing module 24 , while the main control board 36 performs data collection, calculations, and command output. The display output is connected via the driver board 40 .

[0064] In some embodiments, the reagents include a first substrate reagent and a second substrate reagent. When the semiconductor sequencing chip 14 is immersed in the first substrate reagent or the second substrate reagent, two of the bases are caused to emit light, while the other two bases are not. In this way, four different bases can be distinguished by the luminescence of the two channels.

[0065] Specifically, when the semiconductor sequencing chip 14 is immersed in the first substrate reagent or the second substrate reagent, a biochemical reaction occurs in the first substrate reagent or the second substrate reagent, which is manifested as different luminescence intensities of the bases in the reaction. By limiting the luminescence signal range by the target template 11, the luminescence conditions of the bases in the first substrate reagent or the second substrate reagent can be obtained, thereby distinguishing different bases.

[0066] In some embodiments, referring to FIG4 , the target template 11 includes a first signal range 13 , a second signal range 15 , a third signal range 17 , and a fourth signal range 19 , and the types of bases include a first type, a second type, a third type, and a fourth type.

[0067] The first signal range 13 indicates that the first type of base does not emit light in the first substrate reagent and the second substrate reagent;

[0068] The second signal range 15 indicates that the second type of base does not emit light in the first substrate reagent but emits light in the second substrate reagent;

[0069] The third signal range 17 indicates that the third type of base emits light in the first substrate reagent but does not emit light in the second substrate reagent;

[0070] The fourth signal range 19 indicates that the fourth type of base emits light in both the first substrate reagent and the second substrate reagent. In this way, the specific type of base can be determined in the biochemical reaction.

[0071] Specifically, the target template 11 determined by the data output by the first core row 44 includes a first signal range 13, a second signal range 15, a third signal range 17 and a fourth signal range 19. The four bases react in the first substrate reagent or the second substrate reagent to exhibit different luminescence intensities. The signal range defined by the target template 11 outputs two signals, luminescent or non-luminescent, and the reaction results of each base in the two substrate reagents are unique, thereby accurately determining the type of the current base.

[0072] In certain embodiments, the sequencing method comprises:

[0073] The intercept classification algorithm is used to classify the data output by the remaining core rows 44 into the signal range of the target template 11. In this way, sequencing errors can be reduced and more accurate sequencing results can be obtained.

[0074] Specifically, the data read out by the first core row 44 after the reaction is completed in the reagent can be used to obtain a signal scatter plot on the coordinate axis. The two coordinate axes represent the luminescence intensity of the base in the two substrate reagents. The scatter points in the coordinate axis are mostly concentrated in four areas according to the different luminescence conditions of the base. By analyzing and processing the four scatter point concentration areas and outlining the scattered points along the outer circle of each concentrated area, circular (or elliptical) areas representing four different bases can be distinguished on the graph, which are the signal ranges defined by the target template 11, such as the first signal range 13, the second signal range 15, the third signal range 17, and the fourth signal range 19 shown in Figure 4. When reading the remaining rows of data, the target template 11 obtained by the first core row 44 is used as a reference. The intercept classification algorithm is used to classify the data output by the remaining core rows 44 into the signal range of the target template 11. That is, based on the comparison between the position of the read data on the coordinate and the distance (i.e., the intercept) between the center of each circle (or ellipse), the point is classified into the circle (or ellipse) range with the shortest intercept, which can reduce sequencing errors and obtain more accurate sequencing results.

[0075] In certain embodiments, the simplification process includes binarization, which can reduce the amount of data computation while accurately outputting sequencing results.

[0076] Specifically, through the signal range defined by the target template 11, the different luminescence intensities of the read bases are simplified to output two signals of luminescence or non-luminescence, with "0" representing non-luminescence and "1" representing luminescence. Thus, the base reacts in two substrate reagents and can output two luminescence or non-luminescence light signal data, marked as "00", "01", "10" or "11", and different light signal data correspond to different types of bases, as shown in Figure 5. In this way, each pixel finally outputs a 1-bit data, and a 2-bit data is obtained after the two substrates react. The 2-bit data corresponds to one of the four bases of "AGCT", which greatly reduces the data transmission processing pressure. It can be understood that in other embodiments, the simplified processing can also be other simplified processing, and is not limited to binarization processing. The simplified processing can be understood as processing the original data to reduce the output of the data volume. Binarization is not limited to being represented by 0 and 1, and can also be represented by other numerical values ​​or symbols.

[0077] In one example, the semiconductor sequencing chip 14 is loaded row by row under the control of the robot 10 with the base sequence clusters / balls of the starting fragments after the same amplification process, and then the sequencing reagents are immersed in the core row 44 as the immersion unit. When the semiconductor sequencing chip 14 is immersed in the first substrate reagent with the core row 44 as the immersion unit, the 1-bit optical signal data of all the core rows is read out. When the first core row of the semiconductor sequencing chip 14 is immersed in the second substrate reagent, all the 2-bit data of the first core row of the semiconductor sequencing chip 14 are read out, thereby obtaining the target template 11.

[0078] When the second core row of the semiconductor sequencing chip 14 is immersed in the second substrate reagent, the data of the second core row is included in the signal range of the target template 11, and the output 1-bit optical signal data is combined with the 1-bit optical signal data output by the second core row of the semiconductor sequencing chip 14 when it is immersed in the first substrate reagent to form 2-bit optical signal data "00", "01", "10" or "11", corresponding to one of the four bases "AGCT", and the optical signal data of the base on the second core row of the semiconductor sequencing chip 14 can be obtained.

[0079] As the semiconductor sequencing chip 14 is immersed in the second substrate reagent, performing biochemical reactions and reading data in units of core rows 44, until all core rows 44 of the semiconductor sequencing chip 14 are immersed in the second substrate reagent and read, the optical signal data for the first base of all base sequence clusters / globes loaded on the semiconductor sequencing chip 14 is read, and a sequencing cycle is completed. Multiple sequencing cycles are performed through the above sequencing process until the optical signal data for each base in all base sequence clusters / globes is read, completing a sequencing cycle.

[0080] In certain embodiments, a gene sequencing system includes a row switching and common reading unit 34, wherein the row switching and common reading unit 34 is connected to all core rows 44, and a sequencing method includes:

[0081] The data channel switching and data reading of the core 42 immersed in the reagent are controlled by the row switching and common reading unit 34. In this way, the data of the semiconductor sequencing chip 14 can be read out row by row, reducing the difficulty of the computer system in reading, routing, transmitting, caching, and processing data.

[0082] Specifically, the logical relationship between multiple chip cores 42 fabricated on a wafer using a photomask is first defined. In one example, see Figure 6 . Sixty-nine cores 42 are arrayed on a semiconductor sequencing chip 14. By processing the circuitry within these cores 42, the 69 cores 42 are divided into nine core rows 44. Data is read simultaneously from one or more cores 42 in each core row 44. The row switching and common reading unit 34 may include row switching and common reading circuitry. The row switching and common reading unit 34 connects all core rows 44 and reads image signals row by row. Through the interaction of control channels, data is read at least once each time at least one core row 44 is accessed.

[0083] That is, through the combined control of immersion and read, the system load of sequential reads is reduced to 16% of the parallel full-wafer (semiconductor sequencing chip 14) read. Using the above system logic and algorithm, the 10-bit digital value of each pixel is compressed to 2 bits to represent the four ATCG bases. After the data of all cores in the full wafer (semiconductor sequencing chip 14) is normalized by processing the data of the first immersed core, a simplified algorithm is used to obtain the base sequence results. As a result, the system's transmission, calculation, and storage are extremely simple to implement, and the cost is very low.

[0084] In certain embodiments, the sequencing method comprises:

[0085] The time for each core row 44 to be immersed in the reagent is controlled to be the same, so as to ensure that the time difference between the time for the biochemical reaction between the core row 44 and the reagent each time is not more than a preset range.

[0086] Specifically, in a bioluminescent or other enzymatic luminescent signal generation system, enzymes carried by the preceding biochemical reaction on the cores 42 of the semiconductor sequencing chip 14 begin to generate signals upon contact with the substrate. This signal curve is strongly correlated with factors such as temperature and time. By configuring the movement time of the manipulator 10 in the mechanical control module 16, the manipulator 10 clamps the semiconductor sequencing chip 14 and immerses it in the reagent in units of core rows 44. The time difference between each core row 44 immersing in the reagent is controlled to remain within a preset range, ensuring that the biochemical reaction time within each core row 44 is uniform.

[0087] In certain embodiments, the sequencing method comprises:

[0088] The time difference of the data reading time of each core row 44 is controlled not to exceed a preset range, so as to ensure that the signals obtained by all core rows 44 are relatively uniform.

[0089] Specifically, the image processing module 24 is controlled to set the same data reading time, and the time difference of the biochemical reaction of each unit core row 44 immersed in the reagent does not exceed the preset range. The signal is collected at a fixed time after each unit core row 44, which can ensure that the signals obtained from all core rows 44 are relatively uniform.

[0090] In other embodiments, the data reading time set by the control image processing module 24 can also be set to not exceed a preset time range. The preset time range is determined by the time it takes for the biochemical reaction of each core row 44 to occur in the reagent and the preset range. The image processing module 24 collects signals from the immersed portion within the preset time range, ensuring that data is collected from all core rows 44. For example, if the preset range is 0-1s and the core row immersion time is 10s, the preset time range for the data reading time is 10s-11s, thereby ensuring that the time difference between the core row immersion time and the data reading time does not exceed the preset range.

[0091] In certain embodiments, before the semiconductor sequencing chip 14 is immersed in the reagent, the sequencing method further comprises:

[0092] The entire semiconductor sequencing chip 14 is divided into multiple regions 48 parallel to the reagent reservoir 12. Each region 48 contains a core row 44. The correspondence between each region 48 and each unit core row 44 is stored. This allows the robot arm 10 to determine the movement distance and number of each movement when gripping the semiconductor sequencing chip 14.

[0093] Specifically, referring to Figure 7 , the entire semiconductor sequencing chip 14 is divided into multiple regions 48 parallel to the reagent reservoir 12. Each region 48 includes a core row 44. Each region 48 is where the manipulator 10 moves once, immersing the chip into the reagents for biochemical reactions and data reading. By dividing the manipulator 10 into these regions 48, the amount of movement and the number of movements required during each operation of the entire semiconductor sequencing chip 14 are determined. In the embodiment shown in Figure 7 , the entire semiconductor sequencing chip 14 is divided into seven regions.

[0094] In other embodiments, the entire semiconductor sequencing chip 14 is divided into multiple areas 48, each area 48 can be multiple core rows 44. By changing its circuit logic, multiple core rows 44 are used as one area 48 to perform biochemical reactions and read data in one action of immersing reagents controlled by the robot 10.

[0095] In certain embodiments, the manipulator 10 controls the immersion of the semiconductor sequencing chip 14 in the reagents. The continuous exposure time of each unit core row 44 is controlled using a first timing sequence, while the movement time of the manipulator 10 is controlled using a second timing sequence. A waiting time is provided before and after the continuous exposure time of each unit core row 44 in the first timing sequence and between each movement time of the manipulator 10 in the second timing sequence. This ensures that the manipulator 10 remains stationary during the exposure time, resulting in clearer and more accurate image signals.

[0096] Specifically, Figure 11 is a timing diagram captured during a certain period of time during the test. The exposure time is determined by the biochemical reaction light intensity and the signal-to-noise ratio. The exposure time was determined through preliminary experimental testing and calculations. The first timing sequence controls the continuous exposure time of each unit core row 44. A waiting period is set before and after each exposure time (the high-level portion of the first timing sequence). Between the two waiting times, the second timing sequence controls the movement time of the manipulator 10. By controlling the movement of the manipulator 10 through these three timing sequences, the manipulator 10 remains stationary during the exposure time, thereby obtaining a clear and accurate image signal.

[0097] In some embodiments, the data transmission of each unit core row 44 is controlled by a third timing sequence, where the data transmission time of each unit core row 44 in the third timing sequence is after the continuous exposure time of the corresponding core row 44. In this way, data is read after each core row 44 is immersed, achieving combined immersion and reading control, thereby reducing the transmission, buffering, and processing loads of the system.

[0098] Specifically, the manipulator 10 clamps the semiconductor sequencing chip 14 and moves row by row along the direction perpendicular to the reagent tank 12. In the core row 44 of each unit, as the manipulator 10 gradually immerses in the reagent and a biochemical reaction occurs, the exposure control is switched to the reagent immersion area 48, and the image signal is read out through the row switching and common reading unit 34. The data is transmitted step by step to the data channel through the row switching circuit logic, thereby reducing the transmission, caching, and processing load of the system.

[0099] In some embodiments, each core 42 includes a pixel array 51. The pixel array 51 is a single pixel array 51, or the pixel array 51 is composed of at least two sub-pixel arrays 50 spliced ​​together using stitching techniques. In this way, a semiconductor sequencing chip 14 with an ultra-large size and array can be obtained. FIG10 shows a semiconductor sequencing chip 14 with multiple cores stitched together.

[0100] Specifically, referring to FIG8 , the pixel array 51 occupies the center of the core 42, while the peripheral circuits, including the phase-locked loop, the decoder controller and the digital buffer 52, the correlated double sampling circuit and the comparator 54, the readout circuit 56 (including the digital and analog processors, the decoder and the charge mode readout circuit), the decoder and the driver 58 are located around the pixel array 51 or on another wafer to be bonded thereto, as shown in FIG9 . In other embodiments, the pixel array 51 can be formed by splicing several sub-pixel arrays 50. In one example, as shown in FIG10 , the pixel array 51 is obtained by splicing four sub-pixel arrays 50 using stitching techniques, thereby obtaining a chip with a larger area. In the illustrated embodiment, one pixel array 51 includes r*c pixels.

[0101] In summary, each time a core row 44 of an immersion unit is immersed, the data output by that core row 44 is read at least once, reducing the number of cores read in parallel to reading all core rows 44. Through the luminescence reaction of the bases in two substrate reagents, the base type can be output through a simple optical signal. By compressing the 10-bit digital value of each pixel to 2 bits, the four ATCG bases can be represented, and the base sequence result can be obtained using a simplified algorithm. Therefore, the system's transmission, calculation, and storage are extremely simple to implement, and the cost is very low.

[0102] An embodiment of the present invention further provides a data processing system 100 for use in a gene sequencing system. The data processing system 100 includes a semiconductor sequencing chip 14, a control device 26, and a manipulator 10. The semiconductor sequencing chip 14 includes a processing module and multiple cores 42, which are arranged in an array to form multiple core rows 44. The processing module connects the core rows 44 and the control device 26, which is connected to the manipulator 10. The control device 26 is configured to control the manipulator 10 to immerse the semiconductor sequencing chip 14 in reagents used for sequencing reactions, with core rows 44 serving as immersion units. The reagents include at least two substrate reagents. When the semiconductor sequencing chip 14 is immersed in the substrate reagents, the corresponding bases are caused to emit light or not. The processing module is configured to read data output by each core row immersed in the substrate reagent for each N units of the core row immersed, where N>0, until all core rows are immersed in the substrate reagent.

[0103] The data processing system 100, through combined immersion and readout control, immerses the semiconductor sequencing chip 14 into the reagents used for the sequencing reaction, using core rows 44 as immersion units. The bases carried on the semiconductor sequencing chip 14 can exhibit different light intensities through biochemical reactions in the reagents. For example, in one luminescent substrate reagent, only two of the four ATCG bases will emit light or exhibit strong light intensities. In another luminescent substrate reagent, these two bases will not emit light or exhibit weak light intensities, while the light intensities of the other two bases will be opposite. Therefore, using two luminescent substrate reagents, the base type can be determined based on the light intensities of the four ATCG bases.

[0104] The target template 11 is determined using the data output by the first core row 44, and the data output by the remaining core rows 44 are simplified to obtain optical signal data of different bases. This reduces the system load of sequential reading, simplifies system transmission, calculation, and storage, and reduces costs.

[0105] It should be noted that the above explanations of the implementation methods and beneficial effects of the sequencing method are also applicable to the data processing system of this embodiment. To avoid redundancy, they will not be elaborated here.

[0106] In certain embodiments, after reading the data output by the first core row 44, the data output by the first core row 44 is used to determine a target template 11. The target template 11 includes a signal range indicating whether a base emits light. The target template 11 is used to simplify the data output by the remaining core rows 44 to obtain optical signal data for different bases. The control device 26 is configured to determine the base type based on the optical signal data. In this manner, the target template 11 can be used to simplify the data and obtain optical signal data to determine the base type.

[0107] Specifically, after the core row 44 of each immersion unit is immersed in two substrate reagents, all the base sequence clusters / spheres loaded on the semiconductor sequencing chip 14 undergo a biochemical reaction with the substrate reagents. After one sequencing cycle, the 2-bit optical signal data of the first base of all the base sequence clusters / spheres are read out respectively. The data output by the core row 44 of the immersion unit is read, and a target template 11 is determined using the data output by the first core row 44. The signal range of whether the base emits light is limited by the target template 11. The data output by the remaining core rows 44 are simplified using the target template 11 to obtain and output optical signal data of different bases. At this time, 2-bit optical signal data "00", "01", "10" or "11" can be obtained, corresponding to one of the four bases "AGCT". The control device 26 reads and displays the specific base type or base sequence through the output 2-bit optical signal data.

[0108] After multiple sequencing cycles, the optical signal data of each base in all base sequence clusters / spheres loaded on the semiconductor sequencing chip 14 can be obtained in sequence. At this time, the base sequence of the sequenced gene can be obtained, and the sequencing process is completed.

[0109] In some embodiments, the reagents include a first substrate reagent and a second substrate reagent. When the semiconductor sequencing chip 14 is immersed in the first substrate reagent or the second substrate reagent, two of the bases are caused to emit light, while the other two bases are not. In this way, four different bases can be distinguished by the luminescence of the two channels.

[0110] In some embodiments, the target template 11 includes a first signal range 13, a second signal range 15, a third signal range 17, and a fourth signal range 19, and the types of bases include a first type, a second type, a third type, and a fourth type.

[0111] The first signal range 13 indicates that the first type of base does not emit light in the first substrate reagent and the second substrate reagent;

[0112] The second signal range 15 indicates that the second type of base does not emit light in the first substrate reagent but emits light in the second substrate reagent;

[0113] The third signal range 17 indicates that the third type of base emits light in the first substrate reagent but does not emit light in the second substrate reagent;

[0114] The fourth signal range 19 indicates that the fourth type of base emits light in both the first substrate reagent and the second substrate reagent. In this way, the specific type of base can be determined in the biochemical reaction.

[0115] In some embodiments, the processing module is further configured to:

[0116] The intercept classification algorithm is used to classify the data output by the remaining core rows 44 into the signal range of the target template 11. In this way, sequencing errors can be reduced and more accurate sequencing results can be obtained.

[0117] In certain embodiments, the simplification process includes binarization, which can reduce the amount of data computation while accurately outputting sequencing results.

[0118] In certain embodiments, control device 26 includes an image processing module 24 connected to semiconductor sequencing chip 14. Image processing module 24 includes a row switching and common reading unit 34. Row switching and common reading unit 34 is connected to all core rows 44. Control device 26 controls data channel switching and data reading for core rows 44 immersed in reagents via row switching and common reading unit 34. This enables combined immersion and reading control of semiconductor sequencing chip 14, reducing the difficulty of computer systems in reading, routing, transmitting, caching, and processing data.

[0119] In certain embodiments, the control device 26 includes a mechanical control module 16 connected to the manipulator 10. The mechanical control module 16 is configured to control the manipulator 10 so that the time difference between each unit's core row 44 immersed in the reagent does not exceed a predetermined range. This ensures that the biochemical reaction time on each unit's core row 44 remains uniform.

[0120] Specifically, the mechanical control module 16 controls the movement of the manipulator 10 while gripping the semiconductor sequencing chip 14, and controls the immersion of the semiconductor sequencing chip 14 into the reagent, with core rows 44 serving as the unit. The mechanical control module 16 can set the movement time of the manipulator 10. The manipulator 10 grips the semiconductor sequencing chip 14 and immerses the semiconductor sequencing chip 14 into the reagent, with core rows 44 serving as the unit. The difference in the time it takes for all core rows 44 to be immersed in the reagent is controlled to remain within a preset range, ensuring that the biochemical reaction time within each core row 44 is uniform.

[0121] In certain embodiments, the control device 26 includes an image processing module 24 connected to the semiconductor sequencing chip 14. The image processing module 24 includes a row switching and common reading unit 34. The row switching and common reading unit 34 is configured to control the time difference between the data reading times of each core row 44 to not exceed a preset range. This ensures that the signals obtained from all core rows 44 are relatively uniform.

[0122] Specifically, the image processing module 24 is controlled to set the same data reading time, and the time difference of the biochemical reaction of the core row 44 in the reagent each time is immersed does not exceed the preset range. The signal is collected at a fixed time after each row of chip cores 42 is immersed, which can ensure that the signals obtained from all core rows 44 are relatively uniform.

[0123] In certain embodiments, before the semiconductor sequencing chip 14 is immersed in the reagent, the control device 26 is further configured to divide the entire semiconductor sequencing chip 14 into multiple regions 48 parallel to the reagent reservoir 12. Each region 48 contains a core row 44, and the control device 26 stores the correspondence between each region 48 and each core row 44. By dividing the semiconductor sequencing chip 14 into multiple regions 48, the gene sequencing system can determine the amount and number of movements required by the robot arm 10 during each movement of the semiconductor sequencing chip 14.

[0124] Specifically, the entire semiconductor sequencing chip 14 is divided into multiple regions 48 parallel to the reagent reservoir 12. Each region 48 is where the manipulator 10 moves once to immerse itself in the reagents. By dividing the regions 48, the distance and number of movements required for each movement of the manipulator 10 while gripping the semiconductor sequencing chip 14 are determined during a single operation of the entire semiconductor sequencing chip 14.

[0125] In certain embodiments, the control device 26 includes an image processing module 24 connected to the semiconductor sequencing chip 14. The image processing module 24 includes a row switching and common reading unit 34. The row switching and common reading unit 34 is configured to control the continuous exposure time of each unit core row 44 according to a first timing sequence and the movement time of the manipulator 10 according to a second timing sequence. A waiting time is provided before and after the continuous exposure time of each unit core row 44 in the first timing sequence and between each movement time of the manipulator 10 in the second timing sequence. In this manner, the manipulator 10 remains stationary during the exposure time, which can provide clearer and more accurate image signals.

[0126] Specifically, the exposure time is determined by the biochemical reaction light intensity and signal-to-noise ratio. The exposure time, determined through preliminary experimental testing and calculations, is controlled by a first timing sequence for the continuous exposure time of each core row 44. A waiting period is set before and after each exposure time, and a second timing sequence controls the movement time of the manipulator 10 between the two waiting times. These three timing sequences ensure that the manipulator 10 remains stationary during the exposure time, thereby obtaining clear and accurate image signals.

[0127] In some embodiments, the row switching and common reading unit 34 is further configured to control the data transmission of each unit of core row 44 using a third timing sequence, wherein the data transmission time of each unit of core row 44 in the third timing sequence is after the continuous exposure time of the corresponding core row 44. In this manner, data is read after each core row 44 is immersed, achieving combined immersion and reading control, thereby reducing the transmission, buffering, and processing loads of the system.

[0128] Specifically, the manipulator 10 clamps the semiconductor sequencing chip 14 and moves row by row along the direction perpendicular to the reagent tank 12. In the core row 44 of each unit, as the manipulator 10 gradually immerses in the reagent and a biochemical reaction occurs, the exposure control is switched to the reagent immersion area 48, and the image signal is read out through the row switching and common reading unit 34. The data is transmitted step by step to the data channel through the row switching circuit logic, thereby reducing the transmission, caching, and processing load of the system.

[0129] In summary, the sequencing method of the semiconductor sequencing chip 14 provided in the embodiment of the present invention is used in a gene sequencing system. Through the control of the sequencing system, the semiconductor sequencing chip 14 is implemented to react with the reagent with the core row 44 as the immersion unit and synchronously read the data, and then the read data is calculated. The target template 11 obtained according to the data of the first core row 44 is used to limit the signal range of the subsequent read data, thereby outputting a 2-bit signal to determine the base type, reducing the system load of sequential reading, and relatively simply realizing the system transmission, calculation, and storage, and also reducing costs.

[0130] An embodiment of the present invention further provides a gene sequencing system. The above description of the implementation and beneficial effects of the data processing system of the semiconductor sequencing chip 14 is also applicable to the gene sequencing system used in the embodiment of the present invention. To avoid redundancy, it will not be elaborated here.

[0131] Throughout this specification, reference to terms such as "one embodiment," "some embodiments," "illustrative embodiments," "examples," "specific examples," or "some examples" means that a specific feature, structure, material, or characteristic described in conjunction with an embodiment or example is included in at least one embodiment or example of the present application. In this specification, the schematic representations of the above terms do not necessarily refer to the same embodiment or example. Furthermore, the specific features, structures, materials, or characteristics described may be combined in any suitable manner in any one or more embodiments or examples.

[0132] Through the description of the above implementation methods, those skilled in the art can clearly understand that the above-mentioned embodiment methods can be implemented by means of software plus the necessary general hardware platform, and of course can also be implemented by hardware, but in many cases the former is a better implementation method. Based on this understanding, the technical solution of the present application, or the part that contributes to the prior art, can be embodied in the form of a software product, which is stored in a storage medium (such as ROM / RAM, magnetic disk, optical disk) as mentioned above, and includes a number of instructions for enabling a terminal device (which can be a mobile phone, computer, server, air conditioner, or network device, etc.) to execute the methods of each embodiment of the present application.

[0133] Although the embodiments of the present application have been shown and described above, it can be understood that the above embodiments are illustrative and cannot be understood as limitations on the present application. Ordinary technicians in this field can change, modify, replace and modify the above implementation methods within the scope of the present application.

Claims

1. A sequencing method, characterized in that: For completing sequencing using a semiconductor sequencing chip, the semiconductor sequencing chip comprising a plurality of cores, the plurality of cores being arranged to form a plurality of core rows, the sequencing method comprising: Controlling the semiconductor sequencing chip to contact the reagents used in each round of sequencing reaction in a manner of core behavior contact units, so that the corresponding bases emit light or do not emit light based on the semiconductor sequencing chip contacting the reagents; Based on each core row contacting N units in the reagent, N>0, read the data output by the core row contacting the reagent at least once until all core rows are contacted with the reagent, wherein, after reading the data output by the first core row, determining the target template according to the data output by the first core row, wherein the target template includes a signal range indicating whether the base emits light; Simplifying the data output by the remaining core rows according to the target template to obtain optical signal data of different bases; The base type is determined based on the optical signal data.

2. The sequencing method according to claim 1, wherein The reagents include a first substrate reagent and a second substrate reagent. When the semiconductor sequencing chip contacts the first substrate reagent or the second substrate reagent, two bases therein emit light, while the other two bases do not emit light.

3. The sequencing method according to claim 2, wherein The target module includes a first signal range, a second signal range, a third signal range and a fourth signal range, and the types of bases include a first type, a second type, a third type and a fourth type, wherein, The first signal range indicates that the first type of base does not emit light in both the first substrate reagent and the second substrate reagent; The second signal range indicates that the second type of base does not emit light in the first substrate reagent but emits light in the second substrate reagent; The third signal range indicates that the third type of base emits light in the first substrate reagent but does not emit light in the second substrate reagent; The fourth signal range indicates that a fourth type of base emits light in both the first substrate reagent and the second substrate reagent.

4. The sequencing method according to claim 1, wherein The sequencing method comprises: The switching of data channels contacting the core rows in the reagent and the data reading are controlled by a row switching and common reading unit, which connects all the core rows.

5. The sequencing method according to claim 1, wherein The sequencing method comprises: The time difference of the core rows of each unit contacting the reagent is controlled not to exceed a preset range, or the time difference of the data reading time of each core row of each unit is controlled not to exceed a preset range.

6. The sequencing method according to claim 1, wherein Before the semiconductor sequencing chip is contacted with the reagent, the sequencing method further comprises: The entire semiconductor sequencing chip is divided into multiple areas in a manner parallel to the reagent tank, each area contains one core row, and the corresponding relationship between each area and the core row of each unit is stored.

7. The sequencing method according to claim 1, wherein The semiconductor sequencing chip is controlled to contact the reagent by a robot, the continuous exposure time of the core row of each unit is controlled by a first timing, and the movement time of the robot is controlled by a second timing. A waiting time is separated before and after the continuous exposure time of the core row of each unit in the first timing and each movement time of the robot in the second timing.

8. The sequencing method according to claim 7, characterized in that The data transmission of each unit of the core row is controlled by a third timing sequence, and the data transmission time of each core row in the third timing sequence is after the continuous exposure time of the corresponding core row.

9. The sequencing method according to claim 1, wherein Each of the cores includes a pixel array, which is a single pixel array or is composed of at least two sub-pixel arrays.

10. A data processing system for a gene sequencing system, characterized in that: The data processing system includes a semiconductor sequencing chip, a control device, and a manipulator. The semiconductor sequencing chip includes a processing module and multiple cores. The multiple cores are arranged in an array to form multiple core rows. The processing module connects the core rows and the control device. The control device is connected to the manipulator. The control device is used to: Controlling the manipulator to contact the semiconductor sequencing chip with a reagent used for a sequencing reaction in a manner where the core row is a contact unit, so that bases corresponding to the core row emit light or do not emit light based on the semiconductor sequencing chip contacting the reagent; The processing module is used for: Based on each contact of N units of the core row in the reagent, N>0, data output by the core row contacting the reagent is read at least once until all core rows are contacted with the reagent.

11. The data processing system according to claim 10, wherein: After reading the data output by the first core row, determining a target template according to the data output by the first core row, wherein the target template includes a signal range of whether the base emits light; Simplifying the data output by the remaining core rows according to the target template to obtain optical signal data of different bases; The control device is also used for: determining the types of the bases on the semiconductor sequencing chip based on the exposure of all core rows to the reagent; The base type is determined based on the optical signal data.

12. The data processing system according to claim 10, wherein: The reagents include a first substrate reagent and a second substrate reagent. When the semiconductor sequencing chip contacts the first substrate reagent or the second substrate reagent, two bases therein emit light, while the other two bases do not emit light.

13. The data processing system according to claim 10, wherein: The data output by the remaining core rows are classified into the signal range of the target template through the intercept classification algorithm.

14. The data processing system according to claim 10, wherein: The control device includes an image processing module connected to the semiconductor sequencing chip, the image processing module includes a row switching and common reading unit, the row switching and common reading unit is connected to all core rows, and the control device is used to control the data channel switching and data reading of the core rows in contact with the reagent through the row switching and common reading unit.

15. The data processing system according to claim 10, wherein: The control device includes a mechanical control module connected to the manipulator, and the mechanical control module is used to control the manipulator so that the time difference of each unit core row contacting the reagent does not exceed a preset range.

16. The data processing system according to claim 10, wherein: The control device includes an image processing module connected to the semiconductor sequencing chip, and the image processing module includes a row switching and common reading unit. The row switching and common reading unit is used to control the time difference of the data reading time of the core row of each unit to not exceed a preset range.

17. The data processing system according to claim 10, wherein: Before the semiconductor sequencing chip contacts the reagent, the control device is also used to divide the entire semiconductor sequencing chip into multiple areas in a manner parallel to the reagent tank, each area contains one core row, and stores the correspondence between each area and the core row of each unit.

18. The data processing system according to claim 10, wherein: The control device includes an image processing module connected to the semiconductor sequencing chip, and the image processing module includes a row switching and common reading unit. The row switching and common reading unit is used to control the continuous exposure time of the core row of each unit through a first timing sequence, and control the movement time of the manipulator through a second timing sequence. There is a waiting time before and after the continuous exposure time of the core row of each unit in the first timing sequence and each movement time of the manipulator in the second timing sequence.

19. The data processing system according to claim 18, wherein: The row switching and common reading unit is further configured to control data transmission of each unit core row through a third timing sequence, wherein the data transmission time of each core row in the third timing sequence is after the continuous exposure time of the corresponding core row.

20. A gene sequencing system, characterized in that: A data processing system comprising any one of claims 10-19.

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