CN112397145A - HRD (high resolution display) score calculation method based on chip detection - Google Patents
HRD (high resolution display) score calculation method based on chip detection Download PDFInfo
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- 238000004364 calculation method Methods 0.000 title claims abstract description 59
- 238000001514 detection method Methods 0.000 title claims abstract description 19
- 108700028369 Alleles Proteins 0.000 claims abstract description 16
- 108091035539 telomere Proteins 0.000 claims abstract description 16
- 210000003411 telomere Anatomy 0.000 claims abstract description 16
- 102000055501 telomere Human genes 0.000 claims abstract description 16
- 238000013508 migration Methods 0.000 claims abstract description 12
- 230000005012 migration Effects 0.000 claims abstract description 12
- 238000000034 method Methods 0.000 claims abstract description 9
- 210000000349 chromosome Anatomy 0.000 claims description 10
- 239000012634 fragment Substances 0.000 claims description 6
- 108091081400 Subtelomere Proteins 0.000 claims description 3
- 210000002230 centromere Anatomy 0.000 claims description 3
- 230000002759 chromosomal effect Effects 0.000 claims description 3
- 238000001914 filtration Methods 0.000 claims description 3
- 206010028980 Neoplasm Diseases 0.000 abstract description 15
- 108090000623 proteins and genes Proteins 0.000 abstract description 10
- 230000007547 defect Effects 0.000 abstract description 8
- 210000001519 tissue Anatomy 0.000 abstract description 8
- 238000002744 homologous recombination Methods 0.000 abstract description 7
- 230000006801 homologous recombination Effects 0.000 abstract description 7
- 238000011156 evaluation Methods 0.000 abstract description 4
- 239000012188 paraffin wax Substances 0.000 abstract description 4
- 239000000523 sample Substances 0.000 description 12
- 201000011510 cancer Diseases 0.000 description 4
- 210000004881 tumor cell Anatomy 0.000 description 4
- 108020004414 DNA Proteins 0.000 description 3
- 108700020796 Oncogene Proteins 0.000 description 2
- 102000043276 Oncogene Human genes 0.000 description 2
- 230000008859 change Effects 0.000 description 2
- 238000007405 data analysis Methods 0.000 description 2
- 238000010586 diagram Methods 0.000 description 2
- 238000005516 engineering process Methods 0.000 description 2
- 238000002474 experimental method Methods 0.000 description 2
- 238000000605 extraction Methods 0.000 description 2
- 238000009396 hybridization Methods 0.000 description 2
- 238000003752 polymerase chain reaction Methods 0.000 description 2
- 238000007400 DNA extraction Methods 0.000 description 1
- 230000002159 abnormal effect Effects 0.000 description 1
- 238000000137 annealing Methods 0.000 description 1
- 238000003149 assay kit Methods 0.000 description 1
- 210000004027 cell Anatomy 0.000 description 1
- 238000012217 deletion Methods 0.000 description 1
- 230000037430 deletion Effects 0.000 description 1
- 230000029087 digestion Effects 0.000 description 1
- 230000000694 effects Effects 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 230000004048 modification Effects 0.000 description 1
- 238000012216 screening Methods 0.000 description 1
- 230000007704 transition Effects 0.000 description 1
- 238000005406 washing Methods 0.000 description 1
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
- C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
Abstract
The invention discloses a HRD (high resolution D) score calculation method based on chip detection, which comprises the following specific operation steps of: the method comprises the following steps: establishing a calculation method of genome heterozygosity loss LOH; step two: establishing a calculation method of telomere allele imbalance TAI; step three: establishing a calculation method of large-scale end migration LST; step four: and establishing a HRD calculation method. The invention provides a calculation method of genome heterozygosity loss LOH, a calculation method of telomere allele imbalance TAI, a calculation method of large sheet terminal migration LST and a calculation method of HRD, HRD scoring calculation can be carried out on paraffin samples, HRD of tumor tissues can be evaluated by combining data of Affymetrix oncoScan CNV FFPE gene chips with the HRD evaluation method, and homologous recombination defect states of detected tumor samples can be more accurately judged through HRD scores.
Description
Technical Field
The invention relates to the field of tumor gene detection, in particular to a HRD (high resolution contrast) score calculation method based on chip detection.
Background
The gene chip of Affymetrix OncoScan CNV FFPE can identify copy number change and loss of heterozygosity (LOH) by utilizing a Molecular Inversion Probe (MIP) technology, analyze that MIP probes are used for capturing more than 22 ten thousand SNPs which are uniformly distributed in the whole genome, and the probe density is increased in about 900 oncogenes, the sample size only needs 80ng of FFPE DNA, the copy number of the whole genome and the loss of heterozygosity (LOH) of less than or equal to 10Mb in the genome can be detected, the key oncogenes can be detected by the copy number with high resolution (50-125kb), the copy number change in abnormal cells is detected as low as 25 percent, and the copy number linear range is 50+ copies, because the gene chip of Affymetrix OncoScan CNV FFPE has low price, high detection speed and can cover the whole genome, and the gene chip is widely applied to various gene detections at present.
However, there is no method for comprehensively scoring the Homologous Recombination Defect (HRD) at present, and the state of the homologous recombination defect in a tumor sample to be examined cannot be accurately determined.
Therefore, it is necessary to invent a HRD score calculation method based on chip detection to solve the above problems.
Disclosure of Invention
The HRD score calculation method based on chip detection is capable of performing HRD score calculation on paraffin samples by providing a calculation method for establishing genome heterozygosity loss LOH, a calculation method for establishing telomere allele imbalance TAI, a calculation method for establishing large-chip-end migration LST and a calculation method for establishing HRD, is wide in application range, can evaluate the HRD of tumor tissues by combining data of an Affymetrix OncoScan CNV FFPE gene chip with the HRD evaluation method, and can more accurately judge the homologous recombination defect state of the detected tumor samples through the HRD score so as to solve the defects in the technology.
In order to achieve the above purpose, the invention provides the following technical scheme: a HRD score calculation method based on chip detection specifically comprises the following operation steps:
the method comprises the following steps: establishing a calculation method of genome heterozygosity loss LOH;
step two: establishing a calculation method of telomere allele imbalance TAI;
step three: establishing a calculation method of large-scale end migration LST;
step four: and establishing a HRD calculation method.
Preferably, the calculation method for establishing the genomic heterozygosity loss LOH in the first step specifically comprises the following operation steps:
s1: longer than 15 Mb;
s2: shorter than the number of entire chromosomal LOH regions;
s3: each loss of heterozygosity LOH satisfying the above two conditions is given a score of 1, which is the sum of the counts of the regions on all chromosomes that meet the above definition.
Preferably, the calculation method for establishing the telomere allele imbalance TAI in the second step specifically comprises the following steps:
s1: a transdomain subtelomeric region;
s2: does not cross the central centromere;
s3: an allelic imbalance region greater than 11Mb in length;
s4: each telomere allele imbalance TAI satisfying the above three conditions is scored as 1, and the TAI score is the sum of the counts of the number of the above-defined breakpoints on all chromosomes.
Preferably, the calculation method for establishing the large-scale end migration LST in the third step includes the following specific operation steps:
s1: filtering out fragments smaller than 3 Mb;
s2: number of break points longer than 10 Mb;
s3: each large end-shift LST satisfying the above two conditions is given a score of 1, and the LST score is the sum of the counts of all the regions on the chromosome that meet the above definition.
Preferably, the calculation method for establishing the HRD in the fourth step includes the following specific operation steps:
s1: HRD score ═ LOH score + TAI score + LST score.
In the technical scheme, the invention provides the following technical effects and advantages:
the invention can carry out HRD score calculation on the paraffin sample by providing a calculation method for establishing genome heterozygosity loss LOH, a calculation method for establishing telomere allele imbalance TAI, a calculation method for establishing large sheet terminal migration LST and a calculation method for establishing HRD, has wide application, can evaluate the HRD of the tumor tissue by combining the data of the Affymetrix oncoScan CNV FFPE gene chip with the HRD evaluation method of the invention, can more accurately judge the homologous recombination defect state of the detected tumor sample through the HRD score, does not need to carry out other additional experiments at the same time, only needs 80ng sample amount to be checked, and an operator only needs to operate according to the requirements of the specification, can obtain data within 48 hours, and has the advantages of low cost and convenient and rapid operation.
Drawings
The technical solutions in the embodiments of the present invention will be clearly and completely described below with reference to the drawings in the embodiments of the present invention, and it is obvious that the described embodiments are only a part of the embodiments of the present invention, and not all of the embodiments. All other embodiments, which can be derived by a person skilled in the art from the embodiments given herein without making any creative effort, shall fall within the protection scope of the present invention.
FIG. 1 is a schematic diagram of a method of determining Telomere Allele Imbalance (TAI) according to the invention;
fig. 2 is a schematic diagram of a calculation method for determining large sheet end transition (LST) according to the present invention.
Detailed Description
In order to make the technical solutions of the present invention better understood, those skilled in the art will now describe the present invention in further detail with reference to the accompanying drawings.
Example 1:
the invention provides a HRD score calculation method based on chip detection, which is shown in the figure 1-2 and comprises the following specific operation steps:
1): taking FFPE (Formalin-Fixed and Paraffin-Embedded, FFPE) samples of patients with confirmed Tumor to prepare H & E stained sections, observing the content of Tumor cells (TC%, Tumor Cell Percentage), and determining that the content of Tumor cells is not less than 30%;
2): taking the FFPE sample subjected to the tumor cell content screening in the step 1), and extracting DNA (a commercial FFPE sample DNA extraction kit can be adopted), wherein the extraction concentration is required to be not lower than 12 ng/mu L, and the extraction volume is not lower than 6.6 mu L;
3): using Affymetrix
CNV FFPE Assay Kit 2) extracting DNA solution, annealing (Anneal), Gap filling (Gap Fill), first stage polymerase chain reaction (1st PCR), second stage polymerase chain reaction (2nd PCR), digestion (Hae III Digest), Hybridization (Hybridization), washing (Wash)&Stain), scanning (Scan), Data Analysis (Data Analysis) and the like to obtain information including chromosome numbers, fragment copy numbers, heterozygosity deletion states, fragment starting positions, fragment sizes and the like;
4): the calculation was performed as follows:
the method comprises the following steps: the calculation method for establishing the genome heterozygosity loss LOH in the first step comprises the following specific operation steps:
s1: longer than 15 Mb;
s2: shorter than the number of entire chromosomal LOH regions;
s3: each loss of heterozygosity LOH satisfying the above two conditions is given a score of 1, the LOH score being the sum of the counts of the regions on all chromosomes that meet the above definition;
step two: and (2) establishing a calculation method of the telomere allele imbalance TAI, wherein the calculation method for establishing the telomere allele imbalance TAI in the step two specifically comprises the following operation steps:
s1: a transdomain subtelomeric region;
s2: does not cross the central centromere;
s3: an allelic imbalance region greater than 11Mb in length;
s4: each telomere allele imbalance TAI satisfying the above three conditions is counted as 1 point, and the TAI score is the sum of the counts of the number of the broken points on all chromosomes which meet the above definition;
step three: the method for calculating the large-scale end migration LST comprises the following specific operation steps:
s1: filtering out fragments smaller than 3 Mb;
s2: number of break points longer than 10 Mb;
s3: each large end migration LST satisfying the above two conditions is counted as 1, and the LST score is the sum of counts of regions on all chromosomes that meet the above definition;
step four: the HRD establishment calculation method comprises the following specific operation steps:
s1: HRD score ═ LOH score + TAI score + LST score.
The invention also provides an application of the HRD score calculation method based on chip detection as shown in the figures 1-2, which is as follows:
s1: judging the status of Homologous Recombination Defects (HRD) in different cancer species tissues;
s2: a gene detection report for evaluating the HRD state needs to be provided according to the HRD score of the detected sample;
s3: judging the status of loss of heterozygosity (LOH) of the genome in different cancer species tissues;
s4: determining the status of Telomere Allele Imbalance (TAI) in different cancer tissues;
s5: judging the status of large terminal migration (LST) in different cancer tissues.
In the embodiment, by establishing a calculation method for genome heterozygosity loss LOH, a calculation method for establishing telomere allele imbalance TAI, a calculation method for establishing large sheet terminal migration LST and a calculation method for establishing HRD, HRD scoring calculation can be carried out on paraffin samples, the application is wide, HRD of tumor tissues can be evaluated by combining data of Affymetrix oncoScan CNV FFPE gene chips with the HRD evaluation method, the homologous recombination defect state of the detected tumor samples can be more accurately judged through the HRD scoring, other additional experiments are not needed, the detection is carried out only by using a sample amount of 80ng, an operator only needs to operate according to the requirements of a specification, data can be obtained within 48 hours, and the method has the advantages of low cost, convenience and quickness in operation.
While certain exemplary embodiments of the present invention have been described above by way of illustration only, it will be apparent to those of ordinary skill in the art that the described embodiments may be modified in various different ways without departing from the spirit and scope of the invention. Accordingly, the drawings and description are to be regarded as illustrative in nature, and not as restrictive, and any modifications, equivalents, improvements and the like that come within the spirit and principles of the invention are intended to be included within the scope of the invention.
Claims (5)
1. A HRD score calculation method based on chip detection is characterized by comprising the following steps: the specific operation steps are as follows:
the method comprises the following steps: establishing a calculation method of genome heterozygosity loss LOH;
step two: establishing a calculation method of telomere allele imbalance TAI;
step three: establishing a calculation method of large-scale end migration LST;
step four: and establishing a HRD calculation method.
2. The HRD score calculation method based on chip detection as claimed in claim 1, wherein: the calculation method for establishing the genome heterozygosity loss LOH in the first step comprises the following specific operation steps:
s1: longer than 15 Mb;
s2: shorter than the number of entire chromosomal LOH regions;
s3: each loss of heterozygosity LOH satisfying the above two conditions is given a score of 1, which is the sum of the counts of the regions on all chromosomes that meet the above definition.
3. The HRD score calculation method based on chip detection as claimed in claim 2, wherein: the calculation method for establishing the telomere allele imbalance TAI in the step two specifically comprises the following operation steps:
s1: a transdomain subtelomeric region;
s2: does not cross the central centromere;
s3: an allelic imbalance region greater than 11Mb in length;
s4: each telomere allele imbalance TAI satisfying the above three conditions is scored as 1, and the TAI score is the sum of the counts of the number of the above-defined breakpoints on all chromosomes.
4. The HRD score calculation method based on chip detection as claimed in claim 3, wherein: the calculation method for establishing the large-piece end migration LST in the third step comprises the following specific operation steps:
s1: filtering out fragments smaller than 3 Mb;
s2: number of break points longer than 10 Mb;
s3: each large end-shift LST satisfying the above two conditions is given a score of 1, and the LST score is the sum of the counts of all the regions on the chromosome that meet the above definition.
5. The HRD score calculation method based on chip detection as claimed in claim 4, wherein: the method for establishing the HRD in the fourth step comprises the following specific operation steps:
s1: HRD score ═ LOH score + TAI score + LST score.
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Cited By (4)
| Publication number | Priority date | Publication date | Assignee | Title |
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| CN112820351A (en) * | 2021-03-01 | 2021-05-18 | 江苏医联生物科技有限公司 | Method for detecting mutation and HRD (high resolution contrast) score guiding medication of tumor patient |
| CN113948151A (en) * | 2021-06-28 | 2022-01-18 | 北京橡鑫生物科技有限公司 | Processing method of low-depth WGS (WGS) offline data |
| CN114067909A (en) * | 2021-11-23 | 2022-02-18 | 深圳基因家科技有限公司 | Method, device and storage medium for correcting homologous recombination defect score |
| CN114067908A (en) * | 2021-11-23 | 2022-02-18 | 深圳基因家科技有限公司 | Method, device and storage medium for evaluating single-sample homologous recombination defects |
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| CN107287285A (en) * | 2017-03-28 | 2017-10-24 | 上海至本生物科技有限公司 | It is a kind of to predict the method that homologous recombination absent assignment and patient respond to treatment of cancer |
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| WO2016025958A1 (en) * | 2014-08-15 | 2016-02-18 | Myriad Genetics, Inc. | Methods and materials for assessing homologous recombination deficiency |
| WO2016135478A1 (en) * | 2015-02-24 | 2016-09-01 | Synergome Limited | Methods for scoring chromosomal instabilities |
| CN107287285A (en) * | 2017-03-28 | 2017-10-24 | 上海至本生物科技有限公司 | It is a kind of to predict the method that homologous recombination absent assignment and patient respond to treatment of cancer |
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Cited By (7)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN112820351A (en) * | 2021-03-01 | 2021-05-18 | 江苏医联生物科技有限公司 | Method for detecting mutation and HRD (high resolution contrast) score guiding medication of tumor patient |
| CN113948151A (en) * | 2021-06-28 | 2022-01-18 | 北京橡鑫生物科技有限公司 | Processing method of low-depth WGS (WGS) offline data |
| CN113948151B (en) * | 2021-06-28 | 2022-07-05 | 北京橡鑫生物科技有限公司 | Processing method of low-depth WGS (WGS) offline data |
| CN114999568A (en) * | 2021-06-28 | 2022-09-02 | 北京橡鑫生物科技有限公司 | Calculation method of telomere allele imbalance TAI |
| CN114067909A (en) * | 2021-11-23 | 2022-02-18 | 深圳基因家科技有限公司 | Method, device and storage medium for correcting homologous recombination defect score |
| CN114067908A (en) * | 2021-11-23 | 2022-02-18 | 深圳基因家科技有限公司 | Method, device and storage medium for evaluating single-sample homologous recombination defects |
| CN114067909B (en) * | 2021-11-23 | 2022-08-30 | 北京吉因加医学检验实验室有限公司 | Method, device and storage medium for correcting homologous recombination defect score |
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