CN115631788A - Gene pure heterozygous deletion detection method and system based on NGS platform - Google Patents
Gene pure heterozygous deletion detection method and system based on NGS platform Download PDFInfo
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Abstract
The application belongs to the technical field of student information analysis, and particularly relates to a gene pure heterozygous deletion detection method and system based on an NGS platform.
Description
Technical Field
The application belongs to the technical field of bioinformatics, and particularly relates to a gene pure heterozygous deletion detection method and system based on an NGS platform.
Technical Field
A heterozygous deletion of a gene refers to the deletion of one of the two copies of the same gene on a pair of homologous chromosomes (FIG. 1), which still exist on the paired chromosome, whereas a homozygous deletion of a gene refers to the complete deletion of both copies of the same gene. A large number of Single Nucleotide Polymorphism (SNP) sites exist on a human genome, and when pure (hybrid) deletion occurs in a gene, the allele frequency of an internal heterozygous SNP site is changed.
In actual clinical tests, the tumor cell content of not all tissue samples is 100%, and part of tissue samples also contain a part of normal cells. As shown in FIG. 2, when the tumor cell content of the tissue sample is 100%, the Copy Number (CN) and Allele Frequency (AF) are both 0 in the case of Homozygous deletion (Homozygoos) and 1 in the case of Heterozygous deletion (Heterozygoos). If the tumor cell content of the tissue sample is less than 100%, the copy number and allele frequency obtained by the NGS method are the result of mixing the tumor cells and normal cells according to a certain proportion (tumor cell content). Wherein nA and nB are the copy number of the secondary allele of the tumor cells, the sum of nA and nB is the copy number of the tumor cells, and Purity is the content of the tumor cells in the tissue sample.
CN＝(nA+nB)×Purity+2×(1-Purity)
For tissue samples with tumor cell content of less than 100%, the copy number of heterozygous deletion is between 1 and 2, the allele frequency is between 0.5 and 1, the copy number of homozygous deletion is between 0 and 2, the allele frequency is 0.5, and the detection of pure heterozygous deletion cannot be completely realized only by detecting the copy number of genes.
Pure heterozygous deletion of genes has important clinical significance for molecular typing and prognosis prediction. As shown in FIG. 3, the central nervous system tumor classification of the world health organization in 2021 (fifth edition) introduced a series of molecular diagnostic indicators based on histological diagnosis, in which pure heterozygous deletions of multiple genes (CDKN 2A/B, SMARCB 1) were involved. In addition, patients with childhood-type high-grade glioma RTK2 develop high frequency of EGFR amplification and CDKN2A/B homozygous deletions, with better prognosis.
The FISH is a common method for clinically detecting pure heterozygous deletion of the gene, but the detection cannot be carried out in the NGS field, and the development of the gene pure heterozygous deletion detection method based on the NGS platform is beneficial to expanding the application range of the NGS in clinical detection, reducing multiple sampling detection and reducing the clinical NGS detection cost.
In view of this, the present application is proposed.
Disclosure of Invention
In order to solve the technical problem, the following technical scheme is provided:
the application firstly provides a gene pure heterozygous deletion detection method, which comprises the following steps:
1) Obtaining the following data: capturing and establishing a library for a sample through a probe, and sequencing to obtain off-line data;
2) Obtaining copy number CN of target gene based on off-line data mix ；
3) Obtaining allele frequency AF of target gene based on off-line data mix ；
4) Obtaining the tumor cell content Purity of the tissue sample based on off-machine data;
5) And correcting the copy number of the target gene minor allele to obtain the pure heterozygous deletion state of the target gene.
Further, in the step 1), the sample is an ex vivo tissue sample;
further, the sequencing is high-throughput sequencing, preferably NGS sequencing.
Further, the probe in step 1) is designed as follows:
designing a probe covering the full length for a gene sequence within 10Kb, and respectively screening SNP loci at the upstream and downstream of the gene sequence and designing the probe;
and screening SNP sites uniformly covered on the target gene for the gene sequence of more than 10Kb, and designing a probe.
Further, the screening of the SNP sites meets the following conditions: the GC content near SNP is 30-70%, the Hardy-Weinberg genetic equilibrium law is satisfied, and the crowd frequency is more than or equal to 1%.
Further, in the step 2), copy number CN of the target gene is obtained by using copy number variation analysis software mix ；
Further, the step 3) obtains the allele frequency AF of the target gene by using the software for analyzing the single nucleotide variation mix ；
Further, the step 4) obtains the tumor cell content Purity of the tissue sample by using tumor cell content analysis software.
Further, in the step 5), the correcting specifically includes: and determining the optimal solution of the copy number of the sub-allele of the target gene by using the tumor cell content Purity of the tissue sample and the copy number nA and nB of the sub-allele under different deletion states, thereby obtaining the pure heterozygous deletion state of the target gene.
Further, in the step 5),
the relationship between the pure heterozygous deletion state of the target gene and the copy number of the minor allele is as follows:
when CN mix When the allele frequency is less than or equal to 2, respectively substituting nA, nB and Purity under different pure heterozygous deletion states into the following formula to calculate the allele frequency theoretical value AF exp And the detected value AF mix Distance AF between dist Taking the pure heterozygous deletion state corresponding to the minor allele copy number combination with the minimum distance as the detection result of the target gene;
when CN mix When the expression level is more than 2, pure heterozygous deletion of the target gene does not occur;
and nA and nB are the copy numbers of the sub-allelic genes in different deletion states.
The application also provides a detection system for gene pure heterozygous deletion, which comprises the following components:
a. acquiring a sequencing data assembly, capturing and establishing a library for a sample through a probe, and sequencing to obtain off-line data;
b. obtaining the copy number CN of the target gene mix A component for obtaining the copy number CN of the target gene mix ；
c. Obtaining allele frequency AF of target gene mix A module for obtaining the allele frequency AF of a target gene mix ；
d. Obtaining a tumor cell content Purity component of the tissue sample, wherein the component is used for the tumor cell content Purity of the tissue sample;
e. minor allele copy number correction component: the component is used for correcting the copy number of the target gene minor allele, and obtaining the pure heterozygous deletion state of the target gene.
The application also provides a construction method of the gene pure heterozygous deletion detection system, which comprises the following steps:
a. preparing a sequencing data acquisition component, capturing and establishing a library for a sample through a probe, and sequencing to obtain off-line data;
b. preparation of copy number for obtaining target Gene CN mix A component for obtaining the copy number CN of the gene of interest mix ；
c. Preparation of allele frequency AF of the Gene of interest mix A module for obtaining the allele frequency AF of a target gene mix ；
d. Preparing a tumor cell content Purity component for obtaining a tissue sample, wherein the component is used for the tumor cell content Purity of the tissue sample;
e. preparing a minor allele copy number correcting component: the component is used for correcting the copy number of the target gene minor allele, and obtaining the pure heterozygous deletion state of the target gene.
Further, in the above-mentioned assembly 1), the sample is an ex vivo tissue sample;
further, in the above module 1), the sequencing is high-throughput sequencing, preferably NGS sequencing.
Further, the probe in the above-mentioned assembly 1) is designed as follows:
designing a probe covering the full length for a gene sequence within 10Kb, and respectively screening SNP loci at the upstream and downstream of the gene sequence and designing the probe;
and screening SNP sites uniformly covered on the target gene for the gene sequence of more than 10Kb, and designing a probe.
Further, the screening of the SNP sites meets the following conditions: the GC content near SNP is 30-70%, the Hardy-Weinberg genetic equilibrium law is satisfied, and the crowd frequency is more than or equal to 1%.
Further, the above-mentioned component 2) uses copy number variation analysis software to obtain the copy number CN of the target gene mix ；
Further, the above-mentioned component 3) uses SNP analysis software to obtain the allele frequency AF of the target gene mix ；
Further, the above-mentioned component 4) obtains the tumor cell content Purity of the tissue sample using tumor cell content analysis software.
Further, in the above-mentioned component 5), the correcting specifically includes:
and determining the optimal solution of the copy number of the sub-allele of the target gene by using the tumor cell content Purity of the tissue sample and the copy number nA and nB of the sub-allele under different deletion states, thereby obtaining the pure heterozygous deletion state of the target gene.
Further, in the above-mentioned module 5),
the relationship between the pure heterozygous deletion state of the target gene and the copy number of the minor allele is as follows:
when CN mix When the purity is less than or equal to 2, respectively purifying the different materialsSubstituting nA, nB and Purity under the condition of heterozygous deletion into the following formula to calculate the allele frequency theoretical value AF exp And the detected value AF mix Distance AF between dist Taking the pure heterozygous deletion state corresponding to the minor allele copy number combination with the minimum distance as the detection result of the target gene;
when CN mix When the expression level is more than 2, pure heterozygous deletion of the target gene does not occur;
and the nA and the nB are copy numbers of sub-allelic genes in different deletion states.
The present application also provides a computer readable medium having a computer program stored thereon, which when executed by a processor, implements the method of any of the above.
The application also provides an electronic device, comprising a processor and a memory, wherein the memory stores one or more readable instructions, and when the one or more readable instructions are executed by the processor, the method of any one of the above methods is implemented
The beneficial technical effect of this application:
1) The application develops a gene pure heterozygous deletion detection method based on an NGS platform, and solves the problem that the NGS platform can not effectively detect the gene pure heterozygous deletion;
2) The method provides a brand-new probe design method aiming at the genes with different length types, enhances the signals of allele frequency and improves the detection sensitivity;
3) The method and the device simultaneously use the copy number and the allele frequency of the target gene to detect pure heterozygous deletion based on the copy number of the sub-allele gene in the tumor cell, thereby improving the detection accuracy.
Drawings
FIG. 1, schematic diagram of pure heterozygous deletion of a gene;
FIG. 2 copy number and allele frequency of tissue samples at different tumor cell contents;
FIG. 3, pure heterozygous deletion of gene and typing of tumor molecules;
FIG. 4, probe design strategy for target genes;
FIG. 5, flow diagram for pure heterozygous deletion detection;
FIG. 6, pure heterozygous deletion status and minor allele copy number;
FIG. 7, visualization of CDKN2A gene heterozygous deletion;
fig. 8, CDKN2A gene homozygous deletion visualization.
Detailed Description
Embodiments of the present application will be described in detail below with reference to examples, but those skilled in the art will appreciate that the following examples are only illustrative of the present application and should not be construed as limiting the scope of the present application. The examples, in which specific conditions are not specified, were conducted under conventional conditions or conditions recommended by the manufacturer. The reagents or instruments used are conventional products which are not indicated by manufacturers and can be obtained by market purchase.
Definitions of terms, unless defined otherwise below, all technical and scientific terms used in the detailed description of the present application are intended to have the same meaning as commonly understood by one of ordinary skill in the art. While the following terms are believed to be well understood by those skilled in the art, the following definitions are set forth to better explain the present application.
The term "about" in the present application denotes an interval of accuracy that can be understood by a person skilled in the art, which still guarantees the technical effect of the feature in question. The term generally denotes a deviation of ± 10%, preferably ± 5%, from the indicated value.
As used in this application, the terms "comprising," "including," "having," "containing," or "involving" are inclusive or open-ended and do not exclude additional unrecited elements or method steps. The term "consisting of 8230A" is considered to be a preferred embodiment of the term "comprising". If in the following a certain group is defined to comprise at least a certain number of embodiments, this should also be understood as disclosing a group which preferably only consists of these embodiments.
Furthermore, the terms first, second, third, (a), (b), (c), and the like in the description and in the claims, are used for distinguishing between similar elements and not necessarily for describing a sequential or chronological order. It is to be understood that the terms so used are interchangeable under appropriate circumstances and that the embodiments described herein are capable of operation in other sequences than described or illustrated herein.
The gene pure heterozygous deletion detection method described herein essentially comprises the following steps:
1) Obtaining the following data: capturing and establishing a library for a sample through a probe, and sequencing to obtain off-line data;
2) Obtaining copy number CN of target gene based on off-line data mix ；
3) Obtaining allele frequency AF of target gene based on off-line data mix ；
4) Obtaining the tumor cell content Purity of the tissue sample based on off-machine data;
5) And correcting the copy number of the target gene minor allele to obtain the pure heterozygous deletion state of the target gene.
In some embodiments, in step 1), the sample is an ex vivo tissue sample; the sequencing is high throughput sequencing, preferably NGS sequencing.
To enhance the signal at allele frequencies and increase detection sensitivity, in some embodiments, the present application optimizes a probe design method as follows:
designing a probe covering the full length of a gene sequence within 10Kb, and respectively screening SNP sites on the upstream and the downstream of the gene sequence and designing the probe;
and screening SNP sites uniformly covering the target gene for the gene sequence of more than 10Kb, and designing a probe.
The screening of the SNP locus meets the following conditions: the GC content near SNP is 30-70%, the Hardy-Weinberg genetic equilibrium law is satisfied, and the crowd frequency is more than or equal to 1%.
In some embodiments, step 2) described herein can be performed using copy number variation analysis software to obtain the objectiveCopy number of target Gene CN mix ；
In some embodiments, step 3) described herein can use single nucleotide variation analysis software to obtain the allele frequency AF of the target gene mix ；
In some embodiments, step 4) described herein can use tumor cell content analysis software to obtain the tumor cell content Purity of the tissue sample.
In some embodiments, the specific correction of step 5) described herein is: and determining the optimal solution of the copy number of the minor allele of the target gene by using the tumor cell content Purity of the tissue sample and the copy number nA and nB combinations of the minor allele under different deletion states, thereby obtaining the pure heterozygous deletion state of the target gene.
In some embodiments, the relationship between the pure heterozygous deletion state of the target gene and the copy number of the sub-allele in step 5) is as follows:
when CN mix When the allele frequency is less than or equal to 2, respectively substituting nA, nB and Purity under different pure heterozygous deletion states into the following formula to calculate the allele frequency theoretical value AF exp And the detected value AF mix Distance AF between dist Taking the pure heterozygous deletion state corresponding to the minor allele copy number combination with the minimum distance as the detection result of the target gene;
when CN mix When the expression level is more than 2, pure heterozygous deletion of the target gene does not occur;
the application is illustrated below with reference to specific examples.
Example 1 optimization of target Gene Probe design
Detecting pure heterozygous deletion of a gene requires consideration of both copy number of the gene and variation in allele frequency, and therefore, the probe should be designed to cover as much as possible the SNP sites on the target gene. As shown in fig. 4, the present application was designed by searching for:
when designing a probe for a gene having a short length (for example, within 10 Kb), the probe is designed to cover the entire length in consideration of the small number of SNP sites therein, and the SNP site design probe is screened at upstream and downstream (for example, 10 Kb) of the gene to assist in judging the pure heterozygous deletion state of the target gene.
For a gene with a long length (for example, 10Kb or more), the number of SNP sites in the gene is large, and SNP site design probes uniformly covering the target gene are screened.
The screening of SNP loci needs to meet the following conditions: the GC content in the vicinity (such as +/-60 bp) is normal (30-70 percent), the Hardy-Weinberg genetic equilibrium law is satisfied, and the crowd frequency is more than or equal to 1 percent.
Example 2 design of pure hybrid deletion detection method
The pure heterozygous deletion detection method for the target gene is divided into 5 steps, as shown in fig. 5:
a. sequencing a tissue sample on an NGS platform by using the probe designed in the embodiment 1 to obtain off-line original data;
b. obtaining the copy number CN of the target gene by using copy number variation analysis software mix ；
c. Obtaining allele frequency AF of target gene by using mononucleotide variation analysis software mix ；
d. Obtaining the tumor cell content Purity of the tissue sample by using tumor cell content analysis software;
e. the tumor cell content Purity of the tissue sample is used to correct the copy number of the minor allele of the target gene, and the relationship between the pure heterozygous deletion state of the target gene and the copy number of the minor allele is shown in FIG. 6.
When CN mix When the allele frequency is less than or equal to 2, respectively substituting nA, nB and Purity under different pure heterozygous deletion states into a formula to calculate the allele frequency theoretical value AF exp And the detected value AF mix Distance AF between dist Minimum value pair of distanceThe corresponding copy number of the sub-allele (pure heterozygous deletion state) is the optimal solution.
When CN mix When the expression level is higher than 2, the target gene is not subjected to pure heterozygous deletion, so that the pure heterozygous deletion state is normal by default.
Example 3 detection System construction
Based on the gene pure heterozygous deletion detection methods of examples 1 and 2, a detection system of the present application was constructed, which included the following components:
f. acquiring a sequencing data component, designing a probe based on the probe design idea in the embodiment 1, and performing hybridization and library building on a tissue sample and then sequencing to obtain sequencing original data of an NGS platform;
g. obtaining the copy number CN of the target gene mix A component for obtaining the copy number CN of the target gene by using copy number variation analysis software mix ；
h. Obtaining allele frequency AF of target gene mix An assembly for obtaining allele frequency AF of a target gene using single nucleotide variation analysis software mix ；
i. Obtaining a tumor cell content Purity component of the tissue sample, wherein the component obtains the tumor cell content Purity of the tissue sample by using tumor cell content analysis software;
j. minor allele copy number correction component: the component corrects the copy number of the sub-allelic gene of the target gene by using the tumor cell content Purity of the tissue sample; the relationship between the pure heterozygous deletion state of the target gene and the copy number of the sub-allele is shown in FIG. 6.
When CN mix When the allele frequency is less than or equal to 2, respectively substituting nA, nB and Purity under different pure heterozygous deletion states into a formula to calculate the allele frequency theoretical value AF exp And the detected value AF mix Distance AF between dist The copy number of the sub-allele (pure heterozygous deletion state) corresponding to the minimum distance is the optimal solution.
When CN mix When the expression level is higher than 2, pure heterozygous deletion of the target gene does not occur, so that the pure heterozygous deletion state is normal by default.
Example 4 clinical sample-based validation
In order to verify the effectiveness and accuracy of the NGS platform gene pure heterozygous deletion detection method and detection system of the present application, the present example extracts tumor tissues of 16 known neural tumor patients with CDKN2A gene FISH pure heterozygous deletion detection results, determines CDKN2A gene pure heterozygous deletion according to the following method, compares the consistency of NGS and FISH detection results, and specifically comprises the following steps:
1. extracting DNA from the tissue sample, hybridizing by using the probe prepared in the embodiment 1, establishing a library, and sequencing to obtain a target gene sequencing off-machine sequence of each sample;
2. comparing the sequencing result obtained in the step (1) with a reference genome, obtaining the copy number of a target gene in a tissue sample by using copy number variation analysis software, obtaining the allele frequency of the target gene by using mononucleotide variation software, and obtaining the tumor cell content of the tissue sample by using tumor cell content analysis software;
3. substituting the combination of the copy numbers of the sub-alleles under different deletion states and the step 2 into an allele frequency distance calculation formula to obtain the distance between a theoretical value and a detection value, comparing the distance corresponding to each combination, and taking the pure heterozygous deletion state corresponding to the combination of the copy numbers of the sub-alleles with the minimum distance as the detection result of the target gene.
| Sample numbering | Gene | Purity of tumor | nA | nB | CN | mBAF | NGS test results | FISH detection results | Whether it is consistent |
| RD115_22041805 | CDKN2A | 0.47 | 1 | 0 | 1.47 | 0.94 | Heterozygous deletion | Heterozygous deletion | Uniformity |
| RD115_22042604 | CDKN2A | 0.76 | 1 | 0 | 1.42 | 0.81 | Heterozygous deletion | Heterozygous deletion | Uniformity |
| RD115_22042607 | CDKN2A | 0.77 | 0 | 0 | 0.72 | 0.53 | Homozygous deletion | Homozygous deletions | Uniformity |
| RD115_22042615 | CDKN2A | 0.78 | 0 | 0 | 0.44 | 0.54 | Homozygous deletions | Homozygous deletions | Uniformity |
| RD115_22042616 | CDKN2A | 0.85 | 0 | 0 | 0.39 | 0.51 | Homozygous deletion | Homozygous deletion | Uniformity |
| RD115_22042620 | CDKN2A | 0.79 | 0 | 0 | 0.38 | 0.6 | Homozygous deletion | Homozygous deletion | Uniformity |
| RD115_22042625 | CDKN2A | 0.7 | 1 | 1 | 1.96 | 0.52 | Is normal | Is normal | Uniformity |
| RD115_22042631 | CDKN2A | 0.89 | 0 | 0 | 0.25 | 0.53 | Homozygous deletion | Homozygous deletion | Uniformity |
| RD115_22041921 | CDKN2A | 0.53 | 0 | 0 | 1.01 | 0.56 | Homozygous deletion | Homozygous deletion | Uniformity |
| RD115_22041925 | CDKN2A | 0.84 | 1 | 1 | 2.08 | 0.53 | Is normal | Is normal | Uniformity |
| RD115_22041928 | CDKN2A | 0.4 | 0 | 0 | 0.28 | 0 | Homozygous deletion | Homozygous deletions | Uniformity |
| RD115_22041929 | CDKN2A | 0.89 | 0 | 0 | 0.22 | 0.54 | Homozygous deletions | Homozygous deletion | Uniformity |
| RD115_22042201 | CDKN2A | 0.48 | 0 | 0 | 1.18 | 0 | Homozygous deletions | Homozygous deletion | Uniformity |
| RD115_22042241 | CDKN2A | 0.81 | 0 | 0 | 0.43 | 0.53 | Homozygous deletion | Homozygous deletion | Uniformity |
| RD115_22042246 | CDKN2A | 0.8 | 0 | 0 | 0.57 | 0.52 | Homozygous deletion | Homozygous deletion | Uniformity |
| RD115_22042507 | CDKN2A | 0.93 | 0 | 0 | 0.08 | 0.67 | Homozygous deletions | Homozygous deletion | Uniformity |
The results of the CDKN2A gene pure heterozygous deletion assay in clinical samples are shown in the table above, and in FIGS. 7-8. It can be seen that in the multi-sample, the detection results of CDKN2A in NGS and FISH are completely consistent, and the accuracy of the method is fully proved to be 100%.
Finally, it should be noted that: the above embodiments are only used to illustrate the technical solutions of the present application, and not to limit the same; although the present application has been described in detail with reference to the foregoing embodiments, it should be understood by those of ordinary skill in the art that: the technical solutions described in the foregoing embodiments may still be modified, or some or all of the technical features may be equivalently replaced; and the modifications or the substitutions do not make the essence of the corresponding technical solutions depart from the scope of the technical solutions of the embodiments of the present application.
Claims (10)
1. A method for detecting pure heterozygous deletion of a gene, which is characterized by comprising the following steps:
1) Obtaining the following data: capturing and building a library for a sample through a probe, and sequencing to obtain off-line data;
2) Obtaining copy number CN of target gene based on off-line data mix ；
3) Obtaining target genes based on offboard dataAllele frequency AF mix ；
4) Obtaining the tumor cell content Purity of the tissue sample based on off-machine data;
5) And correcting the copy number of the minor allele of the target gene to obtain the pure heterozygous deletion state of the target gene.
2. The method of claim 1, wherein:
in the step 1), the sample is an in vitro tissue sample; the sequencing is high throughput sequencing, preferably NGS sequencing.
3. The method according to any one of claims 1-2, wherein:
the probe in step 1) is designed as follows:
designing a probe covering the full length of a gene sequence within 10Kb, and respectively screening SNP loci at the upstream and downstream of the gene sequence and designing the probe;
and screening SNP sites uniformly covered on the target gene for the gene sequence of more than 10Kb, and designing a probe.
4. The method of claim 3, wherein:
the screening of the SNP locus meets the following conditions: the GC content near SNP is 30-70%, the Hardy-Weinberg genetic equilibrium law is satisfied, and the crowd frequency is more than or equal to 1%.
5. The method of claim 1, wherein:
in the step 5), the correcting specifically includes: and determining the optimal solution of the copy number of the sub-allele of the target gene by using the tumor cell content Purity of the tissue sample and the copy number nA and nB of the sub-allele under different deletion states, thereby obtaining the pure heterozygous deletion state of the target gene.
6. The method of claim 5, wherein:
in the step 5), the step of processing the raw material,
the relationship between the pure heterozygous deletion state of the target gene and the copy number of the minor allele is as follows:
when CN mix When the allele frequency is less than or equal to 2, respectively substituting nA, nB and Purity under different pure heterozygous deletion states into the following formula to calculate the allele frequency theoretical value AF exp And the detected value AF mix Distance AF between dist Taking the pure heterozygous deletion state corresponding to the minor allele copy number combination with the minimum distance as the detection result of the target gene;
when CN mix >2, pure heterozygous deletion of the target gene does not occur;
and nA and nB are the copy numbers of the sub-allelic genes in different deletion states.
7. The method of claim 1,
the step 2) obtains the copy number CN of the target gene by using copy number variation analysis software mix ；
The step 3) obtains the allele frequency AF of the target gene by using single nucleotide variation analysis software mix ；
And 4) obtaining the tumor cell content Purity of the tissue sample by using tumor cell content analysis software.
8. A gene pure heterozygous deletion detection system, which is characterized by comprising the following components:
1) Acquiring a sequencing data assembly, capturing and establishing a library for a sample through a probe, and sequencing to obtain off-line data;
2) Obtaining the copy number CN of the target gene mix The components of the device are combined into a whole,the component is used for obtaining the copy number CN of the target gene mix ；
3) Obtaining allele frequency AF of target gene mix A module for obtaining the allele frequency AF of a target gene mix ；
4) Obtaining a tumor cell content Purity component of the tissue sample, wherein the component is used for the tumor cell content Purity of the tissue sample;
5) Minor allele copy number correction component: the component is used for correcting the copy number of the target gene minor allele, and obtaining the pure heterozygous deletion state of the target gene.
9. A computer-readable medium, in which a computer program is stored which, when being executed by a processor, carries out the method of any one of claims 1 to 8.
10. An electronic device comprising a processor and a memory, the memory having stored thereon one or more readable instructions that, when executed by the processor, implement the method of any of claims 1-8.
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| CN113658638A (en) * | 2021-08-20 | 2021-11-16 | 江苏先声医学诊断有限公司 | Detection method and quality control system for homologous recombination defects based on NGS platform |
| WO2022033000A1 (en) * | 2020-08-12 | 2022-02-17 | 臻悦生物科技江苏有限公司 | Method for determining genomic instability based on next-generation sequencing technology, and kit |
| CN114694750A (en) * | 2022-05-31 | 2022-07-01 | 江苏先声医疗器械有限公司 | Single-sample tumor somatic mutation distinguishing and TMB (Tetramethylbenzidine) detecting method based on NGS (Next Generation System) platform |
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Patent Citations (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| JP2000093185A (en) * | 1998-09-25 | 2000-04-04 | National Cancer Center-Japan | Detection of gene deletion |
| WO2022033000A1 (en) * | 2020-08-12 | 2022-02-17 | 臻悦生物科技江苏有限公司 | Method for determining genomic instability based on next-generation sequencing technology, and kit |
| CN113462783A (en) * | 2021-08-17 | 2021-10-01 | 南京先声医学检验实验室有限公司 | Brain glioma chromosome lp/19q detection method based on MassArray nucleic acid mass spectrum and application thereof |
| CN113658638A (en) * | 2021-08-20 | 2021-11-16 | 江苏先声医学诊断有限公司 | Detection method and quality control system for homologous recombination defects based on NGS platform |
| CN114694750A (en) * | 2022-05-31 | 2022-07-01 | 江苏先声医疗器械有限公司 | Single-sample tumor somatic mutation distinguishing and TMB (Tetramethylbenzidine) detecting method based on NGS (Next Generation System) platform |
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