1p19q co-deletion detection method, device and system and storage medium

Abstract

The invention provides a 1p19q co-deletion detection method, device and system and a storage medium, and is applied to the technical field of molecular detection. The method comprises the following steps: acquiring sequencing data of a target sample; according to the sequencing data, respectively calculating to obtain deletion proportions of the 1p chromosome and the 19q chromosome, and average copy values and relative copy values of the 1p chromosome, the 19q chromosome, the 1q chromosome and the 19p chromosome; and analyzing to obtain a detection result of the target sample. The 1p19q co-deletion detection method provided by the invention has remarkable beneficial effects in the aspects of improving the accuracy, stability and comprehensiveness of detection, and is beneficial to in-depth study and correlation investigation of glioma.

Description

Technical Field

[0001] The present application relates to the field of molecular detection technology, and in particular to a detection method, device, system and storage medium for 1p19q co-deletion. Background Art

[0002] Glioma is a malignant primary brain tumor, and its incidence and mortality rate account for a significant proportion of central nervous system tumors. In-depth research and accurate diagnosis of glioma are of great significance in the fields of molecular diagnosis, molecular biology and bioinformatics. With the update of the classification of central nervous system tumors by the World Health Organization, the role of genomic biomarkers such as IDH1 / 2, 1p19q co-deletion and ATRX has become increasingly prominent. These markers are crucial for tumor classification, prognosis assessment and formulation of treatment strategies.

[0003] In the existing technology, fluorescence in situ hybridization (FISH) is the traditional method for detecting 1p / 19q co-deletion. FISH technology locates specific genes or chromosome regions in cells by hybridizing fluorescently labeled DNA probes with target DNA sequences. However, FISH technology has limitations. It cannot distinguish between the deletion of the entire chromosome arm and smaller local deletions, which may lead to false positive results when detecting 1p / 19q co-deletion. In addition, the resolution of FISH is limited and it is difficult to provide more detailed information on genomic changes.

[0004] The development of next-generation sequencing (NGS) technology has provided a new approach for the molecular diagnosis of glioma. NGS technology can provide comprehensive information on genomic changes within a sample, including mutations in genes such as IDH1 / 2, TERT, and TP53, as well as deletions of chromosome arms 1p and 19q. Compared with FISH, NGS technology has higher accuracy and resolution in detecting 1p / 19q co-deletion, and can detect multiple glioma-related molecular biomarkers at one time.

[0005] Although NGS technology has shown advantages in the molecular diagnosis of glioma, its detection method based on 1p19q still faces challenges. Common NGS detection methods include single nucleotide polymorphism (SNP) analysis and copy number variation (CNV) detection. SNP analysis detects dbSNP site information in a specific region and uses bioinformatics algorithms to analyze the heterozygosity and mutation frequency of the site. However, the SNP method has high requirements for the probe design area and requires uniform coverage of the entire chromosome 1p and 19q, which poses challenges to probe design and experimental operations. CNV detection obtains copy number variation information in the 1p and 19q regions by analyzing deduplicated data, but this method is more complicated in data processing and analysis, and is highly dependent on bioinformatics tools.

[0006] In summary, the existing technologies have several defects in the molecular diagnosis of glioma. Although FISH technology is easy to operate, its resolution and accuracy limit its application in accurate diagnosis. Although NGS technology has improved in accuracy and resolution, its detection method still faces challenges in probe design, data processing and analysis. These problems limit the application of existing technologies in the molecular diagnosis of glioma, especially in the accurate detection of 1p19q co-deletion. Therefore, the development of new detection methods to improve the accuracy and efficiency of diagnosis is of great significance for improving the prognosis and treatment of glioma patients. Summary of the invention

[0007] The purpose of the present invention is to provide a detection method for 1p19q co-deletion for non-diagnostic purposes, which uses average copy values ​​and relative copy values ​​to evaluate the 1p chromosome and 19q chromosome of the target sample, thereby avoiding false positives in the test results and improving accuracy.

[0008] In order to achieve the above-mentioned purpose of the present invention, the following technical solutions are particularly adopted:

[0009] In a first aspect, the present invention provides a method for detecting 1p19q co-deletion, comprising:

[0010] Obtain sequencing data of target samples;

[0011] According to the sequencing data, the deletion ratios of chromosome 1p and chromosome 19q, and the average copy values ​​and relative copy values ​​of chromosome 1p, chromosome 19q, chromosome 1q and chromosome 19p are calculated respectively;

[0012] The detection result of the target sample is obtained based on the deletion ratio, the average copy value and the relative copy value analysis.

[0013] In an optional embodiment, the method for calculating the deletion ratio corresponding to the 1p chromosome and the 19q chromosome includes:

[0014] Obtaining all the fragments and lengths of the deleted chromosome 1p and chromosome 19q in the sequencing data;

[0015] Filter out the consecutive missing fragments as segments;

[0016] Obtaining the starting point and the end point of the segment from the sequencing data; and calculating the length of each missing segment according to the starting point and the end point;

[0017] The lengths of all deleted fragments in the 1p chromosome and the 19q chromosome are summed up respectively to obtain the total deletion lengths corresponding to the 1p chromosome and the 19q chromosome;

[0018] Obtaining the whole arm lengths of the chromosome 1p and the chromosome 19q;

[0019] The deletion ratios corresponding to the 1p chromosome and the 19q chromosome are calculated based on the whole arm length and the total deletion length.

[0020] In an optional embodiment, the calculation formula for the deletion ratio corresponding to the 1p chromosome is:

[0021]

[0022] The calculation formula for the deletion ratio corresponding to the 19q chromosome is:

[0023]

[0024] Among them, SR chr1p represents the deletion ratio corresponding to the 1p chromosome; SR chr19q represents the deletion ratio corresponding to the 19q chromosome; chr1p and chr19q represent the 1p chromosome and the 19q chromosome, respectively; length chr1p Represents the entire arm length of the 1p chromosome; length chr19q represents the whole arm length of the 19q chromosome; seg represents the length of a single segment; x and y represent the number of deleted fragments of the 1p chromosome and the 19q chromosome, respectively; represents the total deletion length of the 1p chromosome; Represents the total deletion length of the chromosome 19q.

[0025] In an optional embodiment, the calculation method of the average copy value and the relative copy value of the chromosome 1p, the chromosome 19q, the chromosome 1q and the chromosome 19p comprises:

[0026] Confirming the bin intervals in the 1p chromosome, the 19q chromosome, the 1q chromosome, and the 19p chromosome in the sequencing data, and obtaining the log2 value of the relative copy rate of each of the bin intervals in the 1p chromosome, the 19q chromosome, the 1q chromosome, and the 19p chromosome in the sequencing data;

[0027] According to the log2 value of the relative copy rate, calculate the mean of the relative copy values ​​of all the bin intervals of each chromosome as the average copy value;

[0028] The relative copy value is calculated according to the average copy value.

[0029] In an optional implementation, the calculation formula for the average copy value includes:

[0030]

[0031] Among them, cn 1p ,cn 1q ,cn 19p andcn 19q They respectively represent the average copy values ​​of the 1p chromosome, the 19q chromosome, the 1q chromosome and the 19p chromosome; a, b, c and d respectively represent the number of bin intervals in the 1p chromosome, the 19q chromosome, the 1q chromosome and the 19p chromosome; log2CR represents the log2 value of the relative copy rate of each bin interval.

[0032] In an optional implementation, the calculation formula of the relative copy value includes:

[0033]

[0034] Among them, cn 1p / 1q represents the relative copy value of the 1p chromosome relative to the 1q chromosome; cn 19p / 19q represents the relative copy value of the chromosome 19p relative to the chromosome 19q; cn 1p ,cn 1q ,cn 19p andcn 19q Respectively represent the average copy values ​​of the chromosome 1p, the chromosome 19q, the chromosome 1q and the chromosome 19p.

[0035] In an optional embodiment, the analysis of the detection result of the target sample according to the deletion ratio, the average copy value and the relative copy value includes:

[0036] Determine whether the target sample meets all preset conditions at the same time;

[0037] If yes, the test result of the target sample is determined to be 1p19q co-deletion positive;

[0038] If not, the test result of the target sample is determined to be 1p19q co-deletion negative;

[0039] The preset conditions include:

[0040] A. The missing ratio is greater than 80%;

[0041] B. The average copy value of the 1p chromosome is less than 1.5, and the average copy value of the 19q chromosome is less than 1.569;

[0042] C. The relative copy value of the 1p chromosome relative to the 1q chromosome is less than 0.712, and the relative copy value of the 19p chromosome relative to the 19q chromosome is less than 0.689.

[0043] In a second aspect, the present invention provides a detection device for glioma 1p19q co-deletion, comprising:

[0044] A sequencing module, used to obtain sequencing data of target samples;

[0045] A calculation module, for calculating the deletion ratio of chromosome 1p and chromosome 19q, and the average copy value and relative copy value of chromosome 1p, chromosome 19q, chromosome 1q and chromosome 19p respectively according to the sequencing data;

[0046] An analysis module is used to analyze and obtain the detection result of the target sample according to the deletion ratio, the average copy value and the relative copy value.

[0047] In a third aspect, the present invention provides a computer device, comprising a processor and a memory, wherein the memory stores a computer program, and the processor is used to execute the computer program to implement the method for detecting 1p19q co-deletion described in any one of the aforementioned embodiments.

[0048] In a fourth aspect, the present invention provides a computer storage medium storing a computer program, wherein when the computer program is executed on a processor, the method for detecting 1p19q co-deletion according to any one of the aforementioned embodiments is implemented.

[0049] The embodiments of the present application have the following beneficial effects:

[0050] (1) Improve the molecular stability of detection: The present invention improves the reliability of detection by directly sequencing DNA and utilizing the high stability of DNA molecules. Compared with methods based on RNA or other molecular markers, DNA sequencing data is more stable, reducing false positive or false negative results caused by molecular degradation or labeling errors, thereby improving the accuracy and repeatability of detection.

[0051] (2) Enhanced ability to distinguish deletion types: The present invention can more accurately distinguish whole-arm deletions from partial deletions. This distinction is crucial for diagnosis and prognosis assessment, because whole-arm deletions and partial deletions may have different clinical significance. Through accurate deletion ratio calculation, the present invention can provide more detailed genomic change information, which helps to more accurately diagnose glioma subtypes such as oligodendroglioma.

[0052] (3) Comprehensive diagnosis in accordance with international standards: The present invention supports the combined diagnosis of 1p19q co-deletion and other key genes (such as IDH, TERT, ATRX), which is in line with the classification standards of the World Health Organization (WHO). This comprehensive diagnostic method can provide more comprehensive molecular typing information, helping doctors make more accurate clinical decisions.

[0053] (4) Reducing false positive results: The present invention effectively avoids SNP false positives caused by amplification of 1q or 19p and CNV false positives caused by loss of the entire chromosome by calculating the relative copy values ​​of 1p / 1q and 19q / 19p. This calculation method based on relative copy values ​​reduces the reliance on a single marker and improves the specificity of detection.

[0054] (5) Determination of Cutoff Value in Statistical Sense: The present invention obtains the Cutoff recommended values ​​of relative copy value and average copy value of a single arm through statistical analysis, which are of great reference value for determining the presence or absence of 1p19q co-deletion. This method of determining Cutoff value based on a large amount of data improves the objectivity and standardization level of detection.

[0055] (6) Improve the comprehensiveness and accuracy of detection: Compared with methods based only on SNP heterozygous deletion or simple calculation of CNV, the present invention provides a more comprehensive detection method. It can not only detect 1p and 19q deletions, but also evaluate the copy number changes of the entire chromosome arm, thereby providing more comprehensive genomic change information.

[0056] (7) Reduced reliance on traditional technologies: The present invention reduces reliance on FISH or traditional pathology testing, which may have problems such as complex operation, high cost, and low resolution. The present invention helps promote the advancement of glioma diagnostic technology by providing a new molecular-level detection method.

[0057] In summary, the 1p19q co-deletion detection method provided by the present invention has significant beneficial effects in improving the accuracy, stability and comprehensiveness of detection, which is helpful for in-depth research and correlation investigation of glioma, and can further serve as a reference for clinical decision-making based on other relevant indicators. BRIEF DESCRIPTION OF THE DRAWINGS

[0058] In order to more clearly illustrate the technical solution of the present application, the following is a brief introduction to the drawings required for use in the embodiments. It should be understood that the following drawings only illustrate certain embodiments of the present application and should not be regarded as limiting the scope of protection of the present application. For ordinary technicians in this field, other related drawings can also be obtained based on these drawings without creative work.

[0059] Figure 1 It is a schematic diagram of the structure of the hardware operating environment involved in the embodiment of the 1p19q co-deletion detection method of the present invention;

[0060] Figure 2 This is a schematic diagram of the process of Example 1 of the 1p19q co-deletion detection method of the present invention;

[0061] Figure 3 This is a flow chart of the refinement of step S200 (steps S210 to S260) in Example 2 of the 1p19q co-deletion detection method of the present invention;

[0062] Figure 4 This is a flow chart of the refinement of step S200 (steps S270 to S290) in Example 3 of the 1p19q co-deletion detection method of the present invention;

[0063] Figure 5 This is a schematic diagram of a detailed process of step S300 in Example 4 of the 1p19q co-deletion detection method of the present invention;

[0064] Figure 6 This is a schematic diagram of the relative copy values ​​of 1p / 1q and 19q / 19p in Example 5 of the 1p19q co-deletion detection method of the present invention;

[0065] Figure 7 Schematic diagram of the ROC curve of the relative copy value in Example 5 of the 1p19q co-deletion detection method of the present invention;

[0066] Figure 8 Schematic diagram of the ROC curve of the single-arm cn value (average copy number) in Example 5 of the 1p19q co-deletion detection method of the present invention;

[0067] Fig. 9 Schematic diagram of module connection of the 1p19q co-deletion detection device in an embodiment of the present invention. DETAILED DESCRIPTION

[0068] The embodiments of the present invention are described in detail below, wherein the same or similar reference numerals throughout represent the same or similar elements or elements having the same or similar functions.

[0069] In addition, the terms "first" and "second" are used for descriptive purposes only and should not be understood as indicating or implying relative importance or implicitly indicating the number of the indicated technical features. Therefore, the features defined as "first" and "second" may explicitly or implicitly include one or more of the features. In the description of the present invention, the meaning of "plurality" is two or more, unless otherwise clearly and specifically defined.

[0070] In the present invention, unless otherwise clearly specified and limited, the terms "installed", "connected", "connected", "fixed" and the like should be understood in a broad sense, for example, it can be a fixed connection, a detachable connection, or an integral connection; it can be a mechanical connection or an electrical connection; it can be a direct connection or an indirect connection through an intermediate medium, it can be the internal connection of two elements or the interaction relationship between two elements. For ordinary technicians in this field, the specific meanings of the above terms in the present invention can be understood according to specific circumstances.

[0071] It should be understood that the specific embodiments described herein are only used to explain the present invention, and are not used to limit the present invention.

[0072] like Figure 1 , which is a schematic diagram of the structure of the hardware operating environment of the terminal involved in the embodiment of the present invention.

[0073] The 1p19q co-deletion detection system provided in an embodiment of the present invention may be a PC, or a mobile terminal device such as a smart phone, a tablet computer or a portable computer. The 1p19q co-deletion detection system may include: a processor 1001, such as a CPU, a network interface 1004, a user interface 1003, a memory 1005 and a communication bus 1002. Among them, the communication bus 1002 is used to realize the connection and communication between these components. The user interface 1003 may include a display screen, an input unit such as a keyboard, and a remote control. The user interface 1003 may also include a standard wired interface and a wireless interface. The network interface 1004 may optionally include a standard wired interface and a wireless interface (such as a WI-FI interface). The memory 1005 may be a high-speed RAM memory, or a stable memory, such as a disk memory. The memory 1005 may also be a storage device independent of the aforementioned processor 1001.

[0074] Among them, the processor can be an integrated circuit chip with signal processing capabilities. The processor can be a general-purpose processor, including a central processing unit (CPU), a graphics processing unit (GPU) and a network processor (NP), a digital signal processor (DSP), an application-specific integrated circuit (ASIC), a field programmable gate array (FPGA) or at least one of other programmable logic devices, discrete gates or transistor logic devices, and discrete hardware components. The general-purpose processor can be a microprocessor or the processor can also be any conventional processor, etc., which can implement or execute the disclosed methods, steps and logic block diagrams in the embodiments of the present application.

[0075] The memory may be, but is not limited to, a random access memory (RAM), a read only memory (ROM), a programmable read-only memory (PROM), an erasable programmable read-only memory (EPROM), an electrically erasable programmable read-only memory (EEPROM), etc. The memory is used to store a computer program, and the processor may execute the computer program accordingly after receiving an execution instruction.

[0076] Those skilled in the art will understand that Figure 1 The 1p19q co-deletion detection system shown in the figure does not constitute a limitation thereof, and may include more or less components than shown in the figure, or combine certain components, or arrange the components differently. Figure 1 As shown, the memory 1005 as a computer-readable storage medium may include an operating system, a data interface control program, a network connection program, and a 1p19q co-deletion detection program.

[0077] Example 1

[0078] Reference Figure 2 Embodiment 1 of the present invention provides a method for detecting 1p19q co-deletion, comprising:

[0079] Step S100, obtaining sequencing data of a target sample.

[0080] The above steps involve obtaining sequencing data from the target sample, which can be accomplished through high-throughput sequencing technology (NGS), which can provide detailed information about the DNA sequences in the sample.

[0081] The target sample may be a tumor tissue sample of a patient suspected of having a glioma that needs to be tested.

[0082] Through the above steps, the result obtained is a large amount of raw sequencing data, which contains the genomic information of the target sample, especially the relevant information of chromosome arms 1p, 1q, 19p and 19q. High-throughput sequencing technology can provide comprehensive and high-resolution genomic data, laying the foundation for subsequent precise analysis. Compared with traditional methods such as FISH, NGS technology can provide richer molecular information.

[0083] Step S200, based on the sequencing data, respectively calculate the deletion ratios of chromosome 1p and chromosome 19q, and the average copy values ​​and relative copy values ​​of chromosome 1p, chromosome 19q, chromosome 1q and chromosome 19p.

[0084] Above, 1p, represents the short arm (p arm) of human chromosome 1. In cytogenetics, each chromosome is divided into two arms: a long arm (q arm) and a short arm (p arm). The number "1" indicates that this is chromosome 1, and "p" represents the short arm. 1q, represents the long arm (q arm) of human chromosome 1. The number "1" indicates that this is chromosome 1, and "q" represents the long arm. 19p, represents the short arm (p arm) of human chromosome 19. The number "19" indicates that this is chromosome 19, and "p" represents the short arm. 19q, represents the long arm (q arm) of human chromosome 19. The number "19" indicates that this is chromosome 19, and "q" represents the long arm.

[0085] In the above steps, bioinformatics tools and algorithms are used to analyze the sequencing data, calculate the deletion ratio of chromosome arms 1p and 19q, and the average copy value and relative copy value of 1p, 1q, 19p and 19q. The following results can be obtained:

[0086] (1) The deletion ratio of chromosome arms 1p and 19q indicates the proportion of the genomic part deleted in these regions to the entire chromosome arm.

[0087] (2) The average copy number values ​​of 1p, 1q, 19p, and 19q, indicating the copy number status of these regions.

[0088] (3) Relative copy number value, which is used to evaluate the copy number difference between chromosome arms.

[0089] This step can accurately identify whole-arm deletions and partial deletions, improving the accuracy of diagnosis. The calculation of relative copy numbers helps to distinguish true 1p19q co-deletion from false positive results.

[0090] Step S300, analyzing and obtaining the detection result of the target sample according to the deletion ratio, the average copy value and the relative copy value.

[0091] The above steps involve comprehensively analyzing and obtaining the 1p19q co-deletion detection result of the target sample based on the data obtained in step S200. The result obtained is the final judgment on whether the target sample has 1p19q co-deletion.

[0092] In this step, the comprehensive analysis of the missing ratio, average copy number and relative copy number is combined to improve the accuracy and reliability of the detection and avoid the misjudgment that may be caused by a single detection indicator.

[0093] The 1p19q co-deletion detection method provided by the present invention improves the reliability of detection by directly sequencing DNA and utilizing the high stability of DNA molecules, thereby reducing false positive or false negative results caused by molecular degradation or labeling errors, thereby improving the accuracy and repeatability of detection. In addition, the present invention can more accurately distinguish between whole-arm deletion and partial deletion, which is crucial for diagnosis and prognosis evaluation, because whole-arm deletion and partial deletion may have different clinical significance. Through accurate calculation of deletion ratio, the present invention can provide more detailed genome change information, which helps to more accurately diagnose glioma subtypes such as oligodendroglioma. The present invention also supports the joint diagnosis of 1p19q co-deletion and other key genes (such as IDH, TERT, ATRX), meets the classification standards of the World Health Organization (WHO), provides more comprehensive molecular typing information, and helps doctors make more accurate clinical decisions. By calculating the relative copy values ​​of 1p / 1q and 19q / 19p, the present invention effectively avoids SNP false positives caused by amplification of 1q or 19p, and CNV false positives caused by the loss of the entire chromosome, thereby improving the specificity of detection. In addition, the present invention obtains the Cutoff recommended value of the relative copy value and the average copy value of a single arm through statistical analysis, thereby improving the objectivity and standardization level of the detection. Compared with the method based only on SNP heterozygous deletion or simply calculating CNV, the present invention provides a more comprehensive detection method, which can not only detect the deletion of 1p and 19q, but also evaluate the copy number changes of the entire chromosome arm, thereby providing more comprehensive genomic change information. Finally, the present invention reduces the dependence on FISH or traditional pathological detection. These traditional technologies may have problems such as complex operation, high cost, and low resolution. By providing a new molecular level detection method, it is helpful to promote the advancement of glioma diagnosis technology. In summary, the present invention has significant beneficial effects in improving the accuracy, stability and comprehensiveness of detection, and helps to improve the diagnosis and prognosis evaluation of glioma.

[0094] Example 2

[0095] Reference Figure 3 Based on the above embodiment 1, this embodiment provides a 1p19q co-deletion detection method, in which the calculation method of the deletion ratio corresponding to the 1p chromosome and the 19q chromosome in step S200 includes:

[0096] Step S210, obtaining all the fragments and lengths of the chromosome 1p and the chromosome 19q deleted in the sequencing data.

[0097] The above steps involve identifying the deleted fragments and their lengths on chromosome 1p and chromosome 19q from the sequencing data of the target sample, and the result obtained is a list of all deleted fragments on chromosome 1p and chromosome 19q, including the start and end positions of each fragment.

[0098] This step can accurately identify the specific missing regions in the genome, providing basic data for subsequent calculation of the missing ratio.

[0099] Specifically, bioinformatics tools, such as CNVkit or other copy number variation detection software, can be used to analyze sequencing data and identify missing fragments.

[0100] For example, in the method of this embodiment, the copying status of the tumor sample is detected by using the software CNVkit to obtain the detection result.

[0101] As described above, when CNVkit is used for detection and analysis, the overall copy status of the target sample is detected, so that two files, namely, cnr and cns files, can be obtained.

[0102] The cnr file contains the log2 value of the relative copy rate (log2CR) of the tumor sample in each bin interval. The cns file can be obtained by segmenting the segments using the circular binary segmentation algorithm (CBs) of cnvkit. The cns file contains the copy information of each segment, including its position and size in the genome.

[0103] In this step, you need to obtain all the fragments and lengths of the missing records of chr1p and chr19q in the cns file.

[0104] Step S220, screening out the consecutive missing fragments as segments.

[0105] As described above, continuous deletion fragments are screened out from all deletion fragments. These continuous deletion fragments are called segments, and the result is a list of continuous deletion fragments on chromosomes 1p and 19q. The identification of continuous deletion fragments helps to more accurately assess the biological significance of the deletion, because biologically relevant deletions are often continuous.

[0106] What constitutes a continuous missing segment can be defined by setting thresholds, such as a minimum segment length and / or a maximum gap length.

[0107] Step S230, obtaining the start point and the end point of the segment from the sequencing data; and calculating the length of each missing segment according to the start point and the end point.

[0108] As described above, the start and end positions of each continuous missing segment are determined from the sequencing data. The result obtained is the precise boundary of each segment, that is, the start and end coordinates of each segment. The precise start and end coordinates help to more accurately calculate the length of the missing segment, thereby improving the accuracy of the missing ratio calculation.

[0109] Step S240, summing up the lengths of all deletion fragments in the 1p chromosome and the 19q chromosome respectively to obtain the total deletion lengths corresponding to the 1p chromosome and the 19q chromosome.

[0110] As mentioned above, the lengths of all deletion fragments on chromosome 1p and chromosome 19q are summed to obtain the total deletion length of each chromosome arm, and the result obtained is the total deletion length of chromosome 1p and 19q. The total deletion length is a key parameter for calculating the deletion ratio and helps to evaluate the deletion of the entire chromosome arm.

[0111] Step S250, obtaining the whole arm lengths of the chromosome 1p and the chromosome 19q.

[0112] As described above, the whole arm lengths of chromosome 1p and chromosome 19q are obtained. These data can usually be obtained from a public database, and the results obtained are the whole arm lengths of chromosome 1p and chromosome 19q.

[0113] The above-mentioned public databases may include but are not limited to UCSC Genome Browser, Ensembl or other public genome databases.

[0114] The whole arm length is another key parameter in calculating the missing proportion and helps to standardize the missing data.

[0115] Step S260, calculating the deletion ratios corresponding to the 1p chromosome and the 19q chromosome according to the whole arm length and the total deletion length.

[0116] As described above, the deletion ratio of chromosome 1p and chromosome 19q is calculated based on the total deletion length and the whole arm length. The result is the deletion ratio of chromosome 1p and chromosome 19q, which is a value between 0 and 1, which can represent the ratio of the deletion length to the whole arm length.

[0117] In some embodiments, the calculation formula for the deletion ratio corresponding to the 1p chromosome is:

[0118]

[0119] The calculation formula for the deletion ratio corresponding to the 19q chromosome is:

[0120]

[0121] Among them, SR chr1p represents the deletion ratio corresponding to the 1p chromosome; SR chr19q represents the deletion ratio corresponding to the 19q chromosome; chr1p and chr19q represent the 1p chromosome and the 19q chromosome, respectively; length chr1p Represents the entire arm length of the 1p chromosome; length chr19q represents the whole arm length of the 19q chromosome; seg represents the length of a single segment; x and y represent the number of deleted fragments of the 1p chromosome and the 19q chromosome, respectively; represents the total deletion length of the 1p chromosome; Represents the total deletion length of the chromosome 19q.

[0122] Example 3

[0123] Reference Figure 4 Based on the above embodiment 1, this embodiment provides a 1p19q co-deletion detection method, in which step S200, the calculation method of the average copy value and the relative copy value of the 1p chromosome, the 19q chromosome, the 1q chromosome and the 19p chromosome includes:

[0124] Step S270, confirming the bin intervals in the 1p chromosome, the 19q chromosome, the 1q chromosome and the 19p chromosome in the sequencing data, and obtaining the log2 value of the relative copy rate of each of the bin intervals in the 1p chromosome, the 19q chromosome, the 1q chromosome and the 19p chromosome in the sequencing data.

[0125] As described above, the bin intervals of the 1p, 19q, 1q and 19p chromosome regions are determined in the sequencing data. The bin interval is a continuous segment into which the genome is divided for analyzing copy number variation. The result obtained is the specific location of each bin interval in the 1p, 19q, 1q and 19p chromosome regions. The determination of the bin interval helps to accurately locate and analyze the copy number variation of a specific chromosome region.

[0126] Specifically, genome reference sequences and bioinformatics tools can be used to divide and confirm bin intervals.

[0127] As mentioned above, the log2 values ​​of the relative copy rate of each bin interval are obtained from the sequencing data, which reflect the ratio of the copy number state of each bin interval relative to the reference sample. The result is the log2 value of each bin interval, which is used to calculate the average copy value and the relative copy value.

[0128] Log2 values ​​provide a standardized metric for comparing copy number changes between different samples.

[0129] Bioinformatics software (such as CNVkit) can be used to calculate the relative copy rate of each bin interval and convert it into a log2 value.

[0130] Step S280, calculating the mean of the relative copy values ​​of all the bin intervals of each chromosome according to the log2 value of the relative copy rate as the average copy value.

[0131] As mentioned above, the mean of the relative copy values ​​of all bin intervals of each chromosome (1p, 19q, 1q, 19p) is calculated, and this mean is the average copy value. The result obtained is the average copy value of each chromosome region, which represents the overall copy number status of the region.

[0132] The mean copy number value provides a comprehensive metric for assessing copy number changes across a chromosomal region.

[0133] Step S290: Calculate the relative copy value according to the average copy value.

[0134] As described above, this step involves calculating the relative copy values ​​of 1p / 1q and 19q / 19p based on the calculated average copy value. The results are the relative copy values ​​of 1p / 1q and 19q / 19p, which are used to evaluate the copy number ratio between chromosome arms.

[0135] Relative copy number values ​​help identify copy number changes in specific chromosome arms, which is crucial for diagnosis and prognostic assessment.

[0136] In some embodiments, the calculation formula of the average copy value includes:

[0137]

[0138] Among them, cn 1p ,cn 1q ,cn 19p andcn 19qThey respectively represent the average copy values ​​of the 1p chromosome, the 19q chromosome, the 1q chromosome and the 19p chromosome; a, b, c and d respectively represent the number of bin intervals in the 1p chromosome, the 19q chromosome, the 1q chromosome and the 19p chromosome; log2CR represents the log2 value of the relative copy rate of each bin interval.

[0139] In some embodiments, the calculation formula of the relative copy value includes:

[0140]

[0141] Among them, cn 1p / 1q represents the relative copy value of the 1p chromosome relative to the 1q chromosome; cn 19p / 19q represents the relative copy value of the chromosome 19p relative to the chromosome 19q; cn 1p ,cn 1q ,cn 19p andcn 19q Respectively represent the average copy values ​​of the chromosome 1p, the chromosome 19q, the chromosome 1q and the chromosome 19p.

[0142] Through the methods and steps in this embodiment, a method for comprehensively utilizing sequencing data, bioinformatics analysis and statistical calculation is provided to accurately evaluate the status of 1p19q co-deletion. This method improves the accuracy and reliability of detection and helps to improve the diagnosis and prognosis of glioma.

[0143] Example 4

[0144] Reference Figure 5 Based on the above embodiment 1, a 1p19q co-deletion detection method is provided in this embodiment, wherein step S300, analyzing and obtaining the detection result of the target sample according to the deletion ratio, the average copy value and the relative copy value, comprises:

[0145] Step S310, determining whether the target sample meets all preset conditions at the same time.

[0146] The above steps involve checking whether the test results of the target sample meet all the preset biological and statistical criteria. The result obtained is a judgment on whether the sample meets the 1p19q co-deletion positive.

[0147] By comprehensively considering multiple parameters, the accuracy and reliability of diagnosis are improved.

[0148] A decision algorithm can be designed that will automatically determine whether a sample meets the criteria for 1p19q co-deletion positivity based on preset conditions.

[0149] Step S320: If yes, the detection result of the target sample is determined to be 1p19q co-deletion positive.

[0150] As mentioned above, if the target sample meets all the preset conditions, this step will mark the sample as 1p19q co-deletion positive. The result obtained is 1p19q co-deletion positive, that is, there is 1p19q co-deletion, which is crucial for further analysis and decision-making.

[0151] Step S330: If not, determine that the detection result of the target sample is 1p19q co-deletion negative.

[0152] As mentioned above, if the target sample does not meet all the preset conditions, this step will mark the sample as 1p19q co-deletion negative. The result obtained is 1p19q co-deletion negative, that is, there is no 1p19q co-deletion, which can exclude specific genetic markers and further combine with other indicators for joint analysis.

[0153] The preset conditions include:

[0154] A. The deletion ratio is greater than 80%.

[0155] B. The average copy value of the 1p chromosome is less than 1.5, and the average copy value of the 19q chromosome is less than 1.569.

[0156] C. The relative copy value of the 1p chromosome relative to the 1q chromosome is less than 0.712, and the relative copy value of the 19p chromosome relative to the 19q chromosome is less than 0.689.

[0157] Among the above preset conditions, ABC must be met at the same time to be judged as 1p19q co-deletion positive, otherwise it is 1p19q co-deletion negative. This method provides a systematic and standardized way to evaluate the 1p19q co-deletion status, which helps to improve the consistency and accuracy of diagnosis.

[0158] Example 5

[0159] In order to better illustrate the method provided in the above-mentioned embodiment, the following specific implementation is provided in this embodiment. In this implementation, a 1p19q co-deletion detection workflow is provided, including:

[0160] 1. Build a copy number baseline suitable for the current working environment:

[0161] To ensure the accuracy of the results of CNVKit, the copy number variation detection software CNVKit was used using the white blood cell sample data to construct a copy baseline within the project bed range.

[0162] (1) Centromeres, telomeres, and highly repetitive regions cannot be detected by next-generation sequencing. To prevent these regions from affecting the segment division during cnv calculation, they should be marked before establishing the baseline. The cnvkit.py access subcommand can be used to calculate the regions that can be covered on the genome. All regions recorded in the exclude.bed file of the UCSC database are marked on the reference genome hg38.fa to obtain the in-target regions. cnvkit.py antitarget can obtain the off-target regions in the detection bed by subtracting the in-target regions.

[0163] (2) Calculate the sequencing depth in all control samples. In this example, a white blood cell sample is used as a control sample, and the cnvkit.py coverage subcommand is used to calculate the sequencing depth of the in-target and off-target regions respectively.

[0164] (3) Construct a sequencing distribution model for a normal genome. The depth distribution obtained in Step 2 is corrected for systematic errors such as GC content and weighted for the proportion of repeat regions using the cnvkit.py reference subcommand to generate a reference.cnn baseline file suitable for this panel. At the same time, the in-target and off-target regions are more evenly divided into bin intervals.

[0165] 2. Calculate the 1p19q copy number of the sample:

[0166] The copy status of tumor samples was detected using the software CNVkit.

[0167] (1) Detect the overall copy status of the sample. Input the normal genome copy baseline reference.cnn constructed in Step 3 into the cnvkit.py batch subcommand. This step generates two files: cnr and cns.

[0168] The cnr file contains the log2 value of the relative copy rate (log2CR) of the tumor sample in each bin interval in the baseline of Step 3. The cns file is obtained by segmenting the segment using the circular binary segmentation algorithm (CBs) of cnvkit.

[0169] The cns file contains a copy of each segment, including its location and size in the genome.

[0170] (2) Calculation of key values.

[0171] All the segments and lengths of chr1p and chr19q deletions are recorded in cns. The large segments with continuous deletions are screened out, and the starting point and end point of the segments are obtained in the cns file. The ratio of the total length of all the deleted segments to the arm length of chr1p or chr19q is calculated. Formula 1 and Formula 2 in the above embodiment are used here.

[0172] Then, according to the log2 value in the cnr file, the average copy value and relative copy value of 1p, 1q, 19p, and 19q are calculated using the above-mentioned formula 3 to formula 8.

[0173] 3. Determine the cutoff value and obtain the test results:

[0174] In this example, 132 glioma samples were used to determine the positive and negative of 1p19q co-deletion by combining multiple information such as clinical diagnosis and second-generation sequencing mutations, including 13 positive samples and 119 negative samples.

[0175] All samples are processed through (1) to (2) in step 2 above to obtain corresponding results for threshold determination. Draw the ROC curve as Figure 6 In the curve graph, the relative copy value of 19q / 19p is significantly lower than that of 1p / 1q, so the threshold should be determined based on Chr19 and Chr1, respectively.

[0176] Based on cn 1p ,cn 1q ,cn 1p / 1q ,cn 19q / 19p Four values ​​determine the threshold.

[0177] In the ROC curve, and Andcn 1p =1.503 and cn 19q =1.569, it can significantly distinguish positive and negative samples, such as Figure 7 and Figure 8 shown.

[0178] 4. Determination of 1p19q deletion by clinical sample examination:

[0179] (1) Ensure that the clinical test conditions are consistent with the sample test conditions for establishing the baseline in steps (1) to (3) of step 1. If they are inconsistent, repeat step 1.

[0180] (2) Repeat steps (1) to (2) in step 2 to obtain the cn of the clinical sample. 1p ,cn 1q ,cn 1p / 1q,cn 19q / 19p , determine the conditions defined in step 3. If all are met, the sample is judged to be 1p19q co-deletion positive, that is, there is 1p19q co-deletion. Otherwise, it is 1p19q co-deletion negative.

[0181] It should be noted that the detection method provided in this embodiment is used for non-diagnostic purposes. This non-diagnostic evaluation is used to draw probabilistic conclusions about correlation. It is not directly intended to obtain disease diagnosis results or health status, but is used to further explore and study the correlation between glioma and the actual status of related chromosomes; the test results obtained cannot directly reflect the diagnosis results or health status of the subjects, but need to be combined with other clinical indicators for further comprehensive evaluation and classification.

[0182] In addition, reference Fig. 9 In an embodiment of the present application, a detection device for glioma 1p19q co-deletion is also provided, comprising:

[0183] A sequencing module 10, used to obtain sequencing data of a target sample;

[0184] A calculation module 20 is used to calculate the deletion ratio of chromosome 1p and chromosome 19q, and the average copy value and relative copy value of chromosome 1p, chromosome 19q, chromosome 1q and chromosome 19p respectively according to the sequencing data;

[0185] The analysis module 30 is used to analyze and obtain the detection result of the target sample according to the deletion ratio, the average copy value and the relative copy value.

[0186] It can be understood that the device of this embodiment corresponds to the detection method of glioma 1p19q co-deletion in the above embodiment, and the options in the above embodiment are also applicable to this embodiment, so they will not be repeated here.

[0187] The present application also provides a computer-readable storage medium for storing the computer program used in the above-mentioned computer device. For example, the computer-readable storage medium may include, but is not limited to, various media that can store program codes, such as a USB flash drive, a mobile hard disk, a read-only memory (ROM), a random access memory (RAM), a magnetic disk or an optical disk.

[0188] In several embodiments provided in the present application, it should be understood that the disclosed devices and methods can also be implemented in other ways. The device embodiments described above are merely schematic. For example, the flowcharts and structure diagrams in the accompanying drawings show the possible architecture, functions and operations of the devices, methods and computer program products according to multiple embodiments of the present application. In this regard, each box in the flowchart or block diagram can represent a module, a program segment or a part of a code, and the module, a program segment or a part of a code contains one or more executable instructions for implementing the specified logical function. It should also be noted that in an alternative implementation, the functions marked in the box can also occur in a different order from the order marked in the accompanying drawings. For example, two consecutive boxes can actually be executed substantially in parallel, and they can sometimes be executed in the opposite order, depending on the functions involved. It should also be noted that each box in the structure diagram and / or the flow diagram, and the combination of boxes in the structure diagram and / or the flow diagram, can be implemented with a dedicated hardware-based system that performs a specified function or action, or can be implemented with a combination of dedicated hardware and computer instructions.

[0189] In addition, the functional modules or units in the various embodiments of the present application may be integrated together to form an independent part, or each module may exist separately, or two or more modules may be integrated to form an independent part.

[0190] If the function is implemented in the form of a software function module and sold or used as an independent product, it can be stored in a computer-readable storage medium. Based on this understanding, the technical solution of the present application can be essentially or partly embodied in the form of a software product that contributes to the prior art, and the computer software product is stored in a storage medium, including several instructions for a computer device (which can be a smart phone, a personal computer, a server, or a network device, etc.) to perform all or part of the steps of the method described in each embodiment of the present application. The aforementioned storage medium includes: various media that can store program codes, such as a USB flash drive, a mobile hard disk, a read-only memory (ROM), a random access memory (RAM), a disk or an optical disk.

[0191] The above description is only a specific implementation manner of the present application, but the protection scope of the present application is not limited thereto. Any technician familiar with the technical field can easily think of changes or substitutions within the technical scope disclosed in the present application, which should be included in the protection scope of the present application.

Claims

1. A method for detecting 1p19q co-deletion, characterized in that: include: Obtain sequencing data of target samples; According to the sequencing data, the deletion ratios of chromosome 1p and chromosome 19q, and the average copy values ​​and relative copy values ​​of chromosome 1p, chromosome 19q, chromosome 1q and chromosome 19p are calculated respectively; The detection result of the target sample is obtained based on the deletion ratio, the average copy value and the relative copy value analysis.

2. The method for detecting 1p19q co-deletion according to claim 1, characterized in that: The calculation method of the deletion ratio corresponding to the 1p chromosome and the 19q chromosome includes: Obtaining all the fragments and lengths of the deleted chromosome 1p and chromosome 19q in the sequencing data; Filter out the consecutive missing fragments as segments; Obtaining the starting point and the end point of the segment from the sequencing data; and calculating the length of each missing segment according to the starting point and the end point; The lengths of all deleted fragments in the 1p chromosome and the 19q chromosome are summed up respectively to obtain the total deletion lengths corresponding to the 1p chromosome and the 19q chromosome; Obtaining the whole arm lengths of the chromosome 1p and the chromosome 19q; The deletion ratios corresponding to the 1p chromosome and the 19q chromosome are calculated based on the whole arm length and the total deletion length.

3. The method for detecting 1p19q co-deletion according to claim 2, characterized in that: The calculation formula for the deletion ratio corresponding to the 1p chromosome is: The calculation formula for the deletion ratio corresponding to the 19q chromosome is: Among them, SR chr1p represents the deletion ratio corresponding to the 1p chromosome; SR chr19q represents the deletion ratio corresponding to the 19q chromosome; chr1p and chr19q represent the 1p chromosome and the 19q chromosome, respectively; length chr1p Represents the entire arm length of the 1p chromosome; length chr19q represents the whole arm length of the 19q chromosome; seg represents the length of a single segment; x and y represent the number of deleted fragments of the 1p chromosome and the 19q chromosome, respectively; represents the total deletion length of the 1p chromosome; Represents the total deletion length of the chromosome 19q.

4. The method for detecting 1p19q co-deletion according to claim 1, characterized in that: The calculation method of the average copy value and the relative copy value of the 1p chromosome, the 19q chromosome, the 1q chromosome and the 19p chromosome comprises: Confirming the bin intervals in the 1p chromosome, the 19q chromosome, the 1q chromosome, and the 19p chromosome in the sequencing data, and obtaining the log2 value of the relative copy rate of each of the bin intervals in the 1p chromosome, the 19q chromosome, the 1q chromosome, and the 19p chromosome in the sequencing data; According to the log2 value of the relative copy rate, calculate the mean of the relative copy values ​​of all the bin intervals of each chromosome as the average copy value; The relative copy value is calculated according to the average copy value.

5. The method for detecting 1p19q co-deletion according to claim 4, characterized in that: The calculation formula of the average copy value includes: Among them, cn 1p ,cn 1q ,cn 19p andcn 19q They respectively represent the average copy values ​​of the 1p chromosome, the 19q chromosome, the 1q chromosome and the 19p chromosome; a, b, c and d respectively represent the number of bin intervals in the 1p chromosome, the 19q chromosome, the 1q chromosome and the 19p chromosome; log2CR represents the log2 value of the relative copy rate of each bin interval.

6. The method for detecting 1p19q co-deletion according to claim 4, characterized in that: The calculation formula of the relative copy value includes: Among them, cn 1p / 1q represents the relative copy value of the 1p chromosome relative to the 1q chromosome; cn 19p / 19q represents the relative copy value of the chromosome 19p relative to the chromosome 19q; cn 1p ,cn 1q ,cn 19p andcn 19q Respectively represent the average copy values ​​of the chromosome 1p, the chromosome 19q, the chromosome 1q and the chromosome 19p.

7. The method for detecting 1p19q co-deletion according to claim 1, characterized in that: The method of obtaining the detection result of the target sample according to the deletion ratio, the average copy value and the relative copy value analysis includes: Determine whether the target sample meets all preset conditions at the same time; If yes, the test result of the target sample is determined to be 1p19q co-deletion positive; If not, the test result of the target sample is determined to be 1p19q co-deletion negative; The preset conditions include: A. The missing ratio is greater than 80%; B. The average copy value of the 1p chromosome is less than 1.5, and the average copy value of the 19q chromosome is less than 1.569; C. The relative copy value of the 1p chromosome relative to the 1q chromosome is less than 0.712, and the relative copy value of the 19p chromosome relative to the 19q chromosome is less than 0.

689.

8. A detection device for glioma 1p19q co-deletion, characterized in that: include: A sequencing module, used to obtain sequencing data of target samples; A calculation module, for calculating the deletion ratio of chromosome 1p and chromosome 19q, and the average copy value and relative copy value of chromosome 1p, chromosome 19q, chromosome 1q and chromosome 19p respectively according to the sequencing data; An analysis module is used to analyze and obtain the detection result of the target sample according to the deletion ratio, the average copy value and the relative copy value.

9. A computer device, characterized in that: The computer device comprises a processor and a memory, wherein the memory stores a computer program, and the processor is configured to execute the computer program to implement the method for detecting 1p19q co-deletion according to any one of claims 1 to 7.

10. A computer storage medium, characterized in that: The device stores a computer program, which, when executed on a processor, implements the method for detecting 1p19q co-deletion according to any one of claims 1 to 7.

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