Method and device for detecting hereditary tumor nucleotide polymorphism and storage medium

Abstract

The embodiment of the invention provides a hereditary tumor nucleotide polymorphism detection method and device and a storage medium, and the method comprises the following steps: obtaining a read sequence and a reference sequence; the reading sequence and the reference sequence are input into a first detection tool and a second detection tool respectively, and a detection method of the first detection tool is based on a second-generation detection technology and comprises the step of reserving a soft shearing sequence and a repetitive sequence; the second detection tool is based on a third-generation detection technology; and combining the detection results of the first detection tool and the second detection tool to obtain a variation detection result. The problem that defects exist in a second-generation detection technology and a third-generation detection technology in the prior art is solved.

Description

TECHNICAL FIELD

[0001] The present document relates to the technical field of molecular biology, and particularly relates to a genetic tumor nucleotide polymorphism detection method, device and storage medium. BACKGROUND

[0002] Gene variations exist universally among different individuals in the same species, and the difference is also the source of genomic polymorphism. Gene variations are mainly divided into three categories: single nucleotide variation, short sequence insertion and deletion variation and large structural variation. The length of short sequence insertion and deletion variation is usually below 50bp.

[0003] At present, the conventional sequencing technology is to detect sequence fragments by using second-generation mutation detection tools and third-generation mutation detection tools.

[0004] However, although the sequence generated by the second-generation sequencing technology has high accuracy, the read length is short (100-150bp), and cannot span most long SV regions, or the insertion and deletion detection of the edge segment of the sequencing sequence is not accurate. Under the third-generation sequencing technology, a sequence of up to 100kbp can be measured, and various gene variations can be easily spanned, but the variation frequency detected by the third-generation detection technology is more than 10%, which is generally high. SUMMARY

[0005] In view of the above scheme, the present application aims to provide a genetic tumor nucleotide polymorphism detection method, device and storage medium to solve at least one of the above technical problems.

[0006] In a first aspect, one or more embodiments of the present specification provide a genetic tumor nucleotide polymorphism detection method, comprising:

[0007] obtaining a read sequence and a reference sequence;

[0008] inputting the read sequence and the reference sequence into a first detection tool and a second detection tool respectively, wherein the detection method of the first detection tool is based on second-generation detection technology, including retaining soft clipping sequences and repeat sequences; the second detection tool is based on third-generation detection technology; and

[0009] merging the detection results of the first detection tool and the second detection tool to obtain a variation detection result.

[0010] Further, the first detection tool allows 200 base mismatches.

[0011] Further, after the variation detection result, the method further comprises:

[0012] removing the detection result with a population frequency higher than 0.1% from the variation detection result.

[0013] Further, the detection results of the first detection tool and the second detection tool are merged, including:

[0014] The detection results of the first detection tool and the second detection tool are taken union.

[0015] Further, after the read sequence and the reference sequence are obtained, before the read sequence and the reference sequence are respectively input into the first detection tool and the second detection tool, the method further includes:

[0016] The read sequence and the reference sequence are subjected to cleaning quality control, and sequences with a sequencing accuracy greater than 99% are retained.

[0017] In a second aspect, an embodiment of the present application provides a device for detecting genetic tumor nucleotide polymorphism, including:

[0018] An acquisition module is configured to acquire a read sequence and a reference sequence.

[0019] A data processing module is configured to input the read sequence and the reference sequence into a first detection tool and a second detection tool respectively, wherein a detection method of the first detection tool is based on second-generation detection technology, including retaining soft clipping sequences and repeat sequences; and the second detection tool is based on third-generation detection technology.

[0020] A merging module is configured to merge detection results of the first detection tool and the second detection tool to obtain variation detection results.

[0021] Further, the device further includes:

[0022] A removing module is configured to remove detection results with a population frequency higher than 0.1% from the variation detection results.

[0023] Further, the merging module is configured to take union of the detection results of the first detection tool and the second detection tool.

[0024] Further, the device further includes:

[0025] A quality control module is configured to subject the read sequence and the reference sequence to cleaning quality control, and retain sequences with a sequencing accuracy greater than 99%.

[0026] In a third aspect, an embodiment of the present application provides a storage medium for storing computer executable instructions, characterized in that the computer executable instructions, when executed, implement steps of the method for detecting genetic tumor nucleotide polymorphism according to any one of the first aspect.

[0027] Compared with the prior art, the present application can at least achieve the following technical effects:

[0028] According to the characteristics of the second generation detection tool and the third generation detection tool, the code of the second generation detection tool is improved (the soft cutting sequence and the repeat sequence are reserved), so that the detection result of the improved second generation detection tool can be perfectly combined with the detection result of the third generation detection tool, thereby improving the detection accuracy. BRIEF DESCRIPTION OF DRAWINGS

[0029] In order to more clearly illustrate the technical solutions in the one or more embodiments of the present specification or the prior art, the drawings needed in the embodiment or prior art description will be briefly introduced below. Obviously, the drawings in the following description are only some embodiments described in the present specification, and those skilled in the art can also obtain other drawings according to these drawings without creative labor.

[0030] Figure 1 A flow chart of a genetic tumor nucleotide polymorphism detection method is provided for one or more embodiments of the present specification.

[0031] Figure 2 A structural schematic diagram of a genetic tumor nucleotide polymorphism detection device is provided for one or more embodiments of the present specification. DETAILED DESCRIPTION

[0032] In order to enable those skilled in the art to better understand the technical solutions in the one or more embodiments of the present specification, the technical solutions in the one or more embodiments of the present specification will be described clearly and completely below with reference to the drawings in the one or more embodiments of the present specification. Obviously, the described embodiments are only some embodiments of the present specification, not all embodiments. Based on the one or more embodiments of the present specification, all other embodiments obtained by those skilled in the art without creative labor should belong to the protection scope of the present document.

[0033] The present application embodiment provides a genetic tumor nucleotide polymorphism detection method, as shown in Figure 1 The method comprises the following steps:

[0034] Step 1, obtaining a read sequence and a reference sequence.

[0035] In the present application embodiment, the sequencing instrument off-line data is cleaned and controlled, and the sequence with a sequencing accuracy greater than a preset value is reserved as a read sequence. At the same time, the reference genome sequence in FASTA format with version HG19 is taken as a reference gene sequence.

[0036] Step 2, inputting the read sequence and the reference sequence into a first detection tool and a second detection tool respectively.

[0037] In an embodiment of the present application, the detection method of the first detection tool is based on the second-generation detection technology, including retaining soft-cut sequences and repeated sequences; the second detection tool is based on the third-generation detection technology.

[0038] It should be noted that soft-clipped sequences are caused by large structural variations and can be found in other alignment positions in the genome. They should be retained for variant detection. Removing them will result in fewer sequences supporting variant detection or a reduced depth of variant detection sites. Third-generation sequencing technology does not involve PCR (polymerase chain reaction) amplification, so the sequenced sequences do not contain repeats, meaning that the measurement results do not include repeats.

[0039] Existing second-generation detection technologies also don't include soft-cut and repeat sequences during their detection process. However, these sequences significantly impact the detection results, so the corresponding operating code of the second-generation detection tool has been modified to ensure that the first-generation tool's detection results retain these sequences.

[0040] Step 3: Combine the detection results of the first detection tool and the second detection tool to obtain a variation detection result.

[0041] In the embodiments of the present application, gene mutation includes the following three types of mutation.

[0042] 1. Single-base variation refers to a situation where the sequencing sequence base is different from the reference genome base at a certain position in the genome, and a single base has mutated.

[0043] 2. Short sequence insertion variation refers to a certain position in the reference genome. When the sequencing sequence is compared with the reference genome sequence, a base sequence of less than 50bp is found to be inserted.

[0044] 3. Short sequence deletion variation refers to the situation where, when the sequencing sequence is compared with the reference genome sequence, a base sequence of less than 50bp is missing at a certain position in the reference genome sequence.

[0045] For the same point, the detection results of the first detection tool and the second detection tool may be different, for example, involving multiple variations. In this case, all of them are used as the detection results.

[0046] In the examples of this application, the first detection tool is limited to allowing 200 base mismatches. Because third-generation sequencing sequences are long, with an average length of over 10K, allowing 200 base mismatches means a mismatch rate of 2%. Compared to the second-generation sequencing read length of 150bp, allowing 8 base mismatches, and a mismatch rate of 5.3% is more stringent, ensuring fewer false positive sites are reported.

[0047] In an embodiment of the present application, after the variation detection results are obtained, the detection results with a population frequency higher than 0.1% are removed from the variation detection results to improve the accuracy of the variation detection results.

[0048] In the embodiment of the present application, merging the detection results of the first detection tool and the second detection tool specifically refers to: taking the union of the detection results of the first detection tool and the second detection tool.

[0049] In order to improve the accuracy of the test results in the embodiment of the present application, the read sequence and the reference sequence are cleaned and quality controlled, and sequences with a sequencing accuracy greater than 99% are retained.

[0050] The present application embodiment provides a device for detecting hereditary tumor nucleotide polymorphisms, such as Figure 2 As shown, including:

[0051] An acquisition module 201 is used to acquire a read sequence and a reference sequence;

[0052] a data processing module 202 for inputting the read sequence and the reference sequence into a first detection tool and a second detection tool, respectively, wherein the detection method of the first detection tool is based on second-generation detection technology, including retaining soft-cut sequences and repeated sequences; and the second detection tool is based on third-generation detection technology; and

[0053] The merging module 203 is configured to merge the detection results of the first detection tool and the second detection tool to obtain a variation detection result.

[0054] In an embodiment of the present application, the apparatus further comprises: a removal module configured to remove detection results having a population frequency higher than 0.1% from the variation detection results.

[0055] In an embodiment of the present application, the merging module is used to obtain a union of the detection results of the first detection tool and the second detection tool.

[0056] In an embodiment of the present application, the apparatus further comprises: a quality control module, configured to perform quality control on the read sequence and the reference sequence, and retain sequences with a sequencing accuracy greater than 99%.

[0057] To illustrate the feasibility of the above solution, this application provides the following examples:

[0058]

[0059] Wherein, #Chrom is a gene fragment, Start is a chromosome start position, refer is a reference base, and call is a variant base. From the result, it can be known that the first detection tool can make up for the deficiency of the second detection tool in the low-frequency result. The second detection tool can make up for the deficiency of the first detection tool in the precision of the high-frequency detection result. That is, based on the first detection tool and the second detection tool, the detection precision can be improved.

[0060] The embodiments of the present application provide a storage medium for storing computer executable instructions, characterized in that the computer executable instructions, when executed, implement the steps of the genetic tumor nucleotide polymorphism detection method in any one of the above embodiments.

[0061] It should be noted that the embodiments of the storage medium in the present specification are based on the same inventive concept as the embodiments of the service providing method based on the blockchain in the present specification, and therefore the specific implementation of this embodiment can be referred to the foregoing implementation of the corresponding service providing method based on the blockchain, and the repeated parts will not be described herein.

[0062] The foregoing describes specific embodiments of the present specification. Other embodiments are within the scope of the appended claims. In some cases, the actions or steps recited in the claims can be performed in a different order than the order in which they are recited in the embodiments and still achieve desirable results. In addition, the processes depicted in the figures do not necessarily require the particular order shown or sequential order to achieve the desired results. In certain implementations, multitasking and parallel processing can be advantageous or possible.

[0063] In the 1930s, it was clear to distinguish whether an improvement in a technology was in hardware (e.g., improvement in circuit structure of diodes, transistors, switches, etc.) or in software (e.g., improvement in method flow). However, as technology has evolved, many improvements in method flow today can be considered as direct improvements in hardware circuit structure. Designers almost always obtain the corresponding hardware circuit structure by programming the improved method flow into the hardware circuit. Therefore, it cannot be said that an improvement in a method flow cannot be implemented by a hardware entity module. For example, a programmable logic device (PLD) (e.g., a field programmable gate array (FPGA)) is an integrated circuit whose logic function is determined by user programming of the device. A digital system is "integrated" on a PLD by the designer programming it, rather than by asking a chip manufacturer to design and fabricate a custom integrated circuit chip. Moreover, instead of manually fabricating an integrated circuit chip, this programming is now mostly implemented by "logic compiler" software, which is similar to software compilers used in program development, and the original code to be compiled is written in a specific programming language, called a hardware description language (HDL), of which there are many, such as ABEL (Advanced Boolean Expression Language), AHDL (Altera Hardware Description Language), Confluence, CUPL (Cornell University Programming Language), HDCal, JHDL (Java Hardware Description Language), Lava, Lola, MyHDL, PALASM, RHDL (Ruby Hardware Description Language), etc., the most commonly used being VHDL (Very-High-Speed Integrated Circuit Hardware Description Language) and Verilog. It should be clear to those skilled in the art that, by simply logically programming a method flow in one of the above hardware description languages and programming it into an integrated circuit, a hardware circuit implementing the logical method flow can be easily obtained.

[0064] The controller can be implemented in any suitable way, for example, the controller can take the form of a microprocessor or processor and a computer readable medium storing computer readable program code, such as software or firmware, executable by the (micro)processor, logic gates, switches, an application specific integrated circuit (ASIC), a programmable logic controller and an embedded microcontroller, examples of which include but are not limited to the following microcontrollers: ARC 625D, Atmel AT91SAM, Microchip PIC18F26K20 and Silicone Labs C8051F320, the memory controller can also be implemented as part of the control logic of the memory. Those skilled in the art will also know that, in addition to implementing the controller purely in terms of computer readable program code, it is possible to implement the controller to perform the same functions using logic gates, switches, application specific integrated circuits, programmable logic controllers and embedded microcontrollers, by logically programming the method steps. The controller can therefore be considered a hardware component, and the means for performing the various functions comprised therein can be considered structures within the hardware component. Alternatively, or even additionally, the means for performing the various functions can be considered both software modules which implement the method and structures within the hardware component.

[0065] The systems, apparatuses, modules or units illustrated by the above embodiments can be implemented by computer chips or entities, or products with certain functions. A typical implementation device is a computer. Specifically, the computer can be a personal computer, a laptop computer, a cellular phone, a camera phone, a smart phone, a personal digital assistant, a media player, a navigation device, an email device, a game console, a tablet computer, a wearable device, or a combination of any of these devices.

[0066] For the sake of description, the above apparatuses are described in various units with functions respectively. Of course, the functions of the units can be implemented in one or more software and / or hardware in the implementation of the embodiments of the present specification.

[0067] Those skilled in the art will appreciate that one or more embodiments of the present specification can be provided as a method, a system or a computer program product. Therefore, one or more embodiments of the present specification can take the form of a complete hardware embodiment, a complete software embodiment, or an embodiment combining software and hardware aspects. Moreover, the present specification can take the form of a computer program product implemented on one or more computer-usable storage media (including but not limited to disk storage, CD-ROMs, optical storage devices, etc.) containing computer usable program code.

[0068] The specification is presented with reference to flow diagrams and / or block diagrams of methods, apparatus (systems) and computer program products according to embodiments of the specification. It will be understood that each block of the flow diagrams and / or block diagrams, and combinations of blocks in the flow diagrams and / or block diagrams, can be implemented by computer program instructions. These computer program instructions can be provided to a processor of a general purpose computer, special purpose computer, embedded processing element or other programmable data processing apparatus to produce a machine, such that the instructions, which execute via the processor of the computer or other programmable data processing apparatus, create means for implementing the functions specified in the flow diagrams and / or block diagrams block or blocks. Figure 1 The flow diagram and / or block diagram in the flow diagrams and / or block diagrams can represent one or more of any appropriate circuitry configured to perform the specified functions. In this regard, one or more flow diagrams and / or block diagrams in the flow diagrams and / or block diagrams can represent a device or devices configured to perform one or more of the functions described herein. Figure 1 The flow diagram and / or block diagram in the flow diagrams and / or block diagrams can represent one or more of any appropriate circuitry configured to perform the specified functions. In this regard, one or more flow diagrams and / or block diagrams in the flow diagrams and / or block diagrams can represent a device or devices configured to perform one or more of the functions described herein.

[0069] The computer program instructions can also be loaded onto a computer or other programmable data processing apparatus to cause a series of operational steps to be performed on the computer or other programmable apparatus to produce a computer implemented process such that the instructions which execute on the computer or other programmable apparatus provide steps for implementing the functions specified in the flow diagrams and / or block diagrams block or blocks. Figure 1 The flow diagram and / or block diagram in the flow diagrams and / or block diagrams can represent one or more of any appropriate circuitry configured to perform the specified functions. In this regard, one or more flow diagrams and / or block diagrams in the flow diagrams and / or block diagrams can represent a device or devices configured to perform one or more of the functions described herein. Figure 1 The flow diagram and / or block diagram in the flow diagrams and / or block diagrams can represent one or more of any appropriate circuitry configured to perform the specified functions. In this regard, one or more flow diagrams and / or block diagrams in the flow diagrams and / or block diagrams can represent a device or devices configured to perform one or more of the functions described herein.

[0070] The computer program instructions can also be loaded onto a computer or other programmable data processing apparatus to cause a series of operational steps to be performed on the computer or other programmable apparatus to produce a computer implemented process such that the instructions which execute on the computer or other programmable apparatus provide steps for implementing the functions specified in the flow diagrams and / or block diagrams block or blocks. Figure 1 The flow diagram and / or block diagram in the flow diagrams and / or block diagrams can represent one or more of any appropriate circuitry configured to perform the specified functions. In this regard, one or more flow diagrams and / or block diagrams in the flow diagrams and / or block diagrams can represent a device or devices configured to perform one or more of the functions described herein. Figure 1 The flow diagram and / or block diagram in the flow diagrams and / or block diagrams can represent one or more of any appropriate circuitry configured to perform the specified functions. In this regard, one or more flow diagrams and / or block diagrams in the flow diagrams and / or block diagrams can represent a device or devices configured to perform one or more of the functions described herein.

[0071] In a typical configuration, a computing device includes one or more processors (CPUs), input / output interfaces, network interfaces, and memory.

[0072] The memory can include non-persistent memory and / or persistent memory, such as flash memory, read-only memory (ROM), and / or volatile or non-volatile random access memory (RAM), among others. The memory is an example of computer-readable media.

[0073] Computer-readable media includes permanent and non-permanent, movable and non-movable media that can be implemented by any method or technology to store information. The information can be computer-readable instructions, data structures, program modules or other data. Examples of computer storage media include, but are not limited to, phase-change memory (PRAM), static random access memory (SRAM), dynamic random access memory (DRAM), other types of random access memory (RAM), read-only memory (ROM), electrically erasable programmable read-only memory (EEPROM), flash memory or other memory technologies, compact disc read-only memory (CD-ROM), digital versatile disc (DVD) or other optical storage, magnetic cassette, magnetic tape, magnetic disk storage or other magnetic storage devices, or any other non-transmission medium that can be used to store information accessible to a computing device. According to the definition herein, computer-readable media does not include transitory media such as modulated data signals and carriers.

[0074] It should also be noted that the terms "comprising", "containing", or any other variant thereof are intended to cover non-exclusive inclusion, such that processes, methods, articles or devices that include a series of elements not only include those elements, but also include other elements not explicitly listed, or inherent to such processes, methods, articles or devices. Without more limitations, the element defined by the statement "comprising a" does not exclude the presence of additional identical elements in the process, method, article or device that includes the element.

[0075] One or more embodiments of the present specification can be described in the general context of computer-executable instructions being executed by a computer, such as program modules. Generally, program modules include routines, programs, objects, components, data structures, and the like that perform particular tasks or implement particular abstract data types. One or more embodiments of the present specification can also be practiced in a distributed computing environment, in which tasks are performed by remote processing devices connected through a communication network. In a distributed computing environment, program modules can be located in both local and remote computer storage media, including storage devices.

[0076] Various embodiments in the present specification are described in a progressive manner, and the same or similar parts between various embodiments can be referred to each other, and each embodiment focuses on the difference from other embodiments. In particular, for system embodiments, since they are basically similar to method embodiments, the description is relatively simple, and the relevant parts can be referred to the part of the method embodiment.

[0077] The above merely provides the example of the present document and is not intended to limit the present document. For those skilled in the art, the present document can have various modifications and changes. Any modification, equivalent replacement, improvement, etc. within the spirit and principle of the present document shall be included in the scope of claims of the present document.

Claims

1. A method for detecting hereditary tumor nucleotide polymorphisms, characterized in that include: Obtain read sequences and reference sequences; Inputting the read sequence and the reference sequence into a first detection tool and a second detection tool, respectively, wherein the detection method of the first detection tool is based on a second-generation detection technology, including retaining soft-cut sequences and repeated sequences; and the second detection tool is based on a third-generation detection technology; as well as The detection results of the first detection tool and the second detection tool are combined to obtain a variation detection result.

2. The method according to claim 1, characterized in that The first detection tool is limited to allow 200 base mismatches.

3. The method according to claim 1, characterized in that After the variant detection results, the method further includes: Detection results with a population frequency higher than 0.1% were removed from the variant detection results.

4. The method according to claim 1, characterized in that Combining the detection results of the first detection tool and the second detection tool includes: The detection results of the first detection tool and the second detection tool are combined.

5. The method according to claim 1, wherein After acquiring the read sequence and the reference sequence, and before inputting the read sequence and the reference sequence into the first detection tool and the second detection tool, respectively, the method further includes: The read sequence and the reference sequence are cleaned and quality controlled, and sequences with a sequencing accuracy greater than 99% are retained.

6. A device for detecting hereditary tumor nucleotide polymorphisms, characterized in that include: an acquisition module for acquiring read sequences and reference sequences; a data processing module, configured to input the read sequence and the reference sequence into a first detection tool and a second detection tool, respectively, wherein the detection method of the first detection tool is based on second-generation detection technology, including retaining soft-cut sequences and repeated sequences; and the second detection tool is based on third-generation detection technology; as well as A merging module is used to merge the detection results of the first detection tool and the second detection tool to obtain a variation detection result.

7. The device according to claim 6, characterized in that The device further comprises: A removal module is used to remove detection results with a population frequency higher than 0.1% from the variation detection results.

8. The device according to claim 6, characterized in that The merging module is used to obtain a union of the detection results of the first detection tool and the second detection tool.

9. The device according to claim 6, characterized in that The device further comprises: The quality control module is used to clean and quality control the read sequence and the reference sequence, and retain sequences with a sequencing accuracy greater than 99%.

10. A storage medium for storing computer-executable instructions, characterized in that: When executed, the computer-executable instructions implement the steps of the method for detecting hereditary tumor nucleotide polymorphisms according to any one of claims 1 to 5.

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