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Microsatellite instability detection method and device based on next-generation sequencing blood samples
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A microsatellite instability and blood sample technology, applied in the field of microsatellite instability detection based on next-generation sequencing blood samples, can solve problems such as instability, difficulty in detecting microsatellites, microsatellite instability detection methods and devices, and achieve Effect of Avoiding False Positive Situations, Avoiding False Negative/False Positive Results
Active Publication Date: 2022-05-20
深圳裕策生物科技有限公司
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[0006] The purpose of the present invention is to provide a method and device for detecting microsatellite instability based on next-generation sequencing blood samples, which solves the problem that it is difficult to detect microsatellite instability when tissues cannot be obtained
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Embodiment 1
[0072] In this embodiment, the samples used are microsatellite instability tissue sample Q2 verified by PCR method, corresponding unverified blood sample Q1, and their control sample Q0. The specific steps of paired sample detection in this embodiment are as follows:
[0073] (1) Scan the genome microsatellite sites to obtain the microsatellite unstable sites to be detected.
[0074] (2) Filter the low-quality loci with an average alignment quality value lower than 50 and the low-coverage loci with a coverage lower than 150 in the two groups of data Q2, Q0 and Q1, Q0, respectively.
[0075] (3) Calculate the microsatellite instability of Q2 relative to Q0 and Q1 relative to Q0.
[0076] (4) Calculate the tumor purity and tumor mutation burden through the somatic mutations of Q2 to Q0 and Q1 to Q0, and output them to the results together with the microsatellite instability in step (3), as shown in Table 1, where it is judged as MSI-h (tissue sample) and bMSI-h (blood sample),...
Embodiment 2
[0080] In this embodiment, the samples used are Microsatellite Stable (MSS) tissue sample K2 verified by PCR method, the corresponding unverified blood sample K1, and their control sample K0. The specific steps of paired sample detection in this embodiment are as follows:
[0081] (1) Scan the genome microsatellite sites to obtain the microsatellite unstable sites to be detected.
[0082] (2) Filter K2, K0 and K1, K0 groups of data with low-quality loci with an average alignment quality value lower than 50 and low-coverage loci with coverage lower than 150, respectively.
[0083] (3) Calculate the microsatellite instability of K2 relative to K0 and K1 relative to K0.
[0084] (4) Calculate the tumor purity and tumor mutation load through the somatic mutations of K2 to K0 and K1 to K0, and output them to the results together with the microsatellite instability in step (3), as shown in Table 2, where it is judged as MSS (tissue sample) and bMSS (blood sample), that is, by the ...
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Abstract
A method and device for detecting microsatellite instability based on next-generation sequencing blood samples, wherein the method includes: acquiring target regions of blood samples to be tested and control samples to capture next-generation sequencing data; finding microsatellite sites from the genome; filtering out The microsatellite sites whose coverage is lower than the set coverage threshold and the microsatellite sites whose comparison quality is lower than the set comparison quality threshold; the number of repetitions of each microsatellite site and the corresponding number of supported sequencing sequences; Standardize the number of repetitions and the number of corresponding supporting sequencing sequences; calculate the absolute value of the difference between the normalized results of the blood samples to be tested and the control samples at each microsatellite site, and calculate the sum of each absolute value, as each microsatellite site Microsatellite instability at microsatellite loci; the mean value of microsatellite instability at all microsatellite loci was calculated as the microsatellite instability of the sample. The invention solves the problem that it is difficult to detect microsatellite instability under the condition that tissues cannot be obtained.
Description
technical field [0001] The invention relates to the technical field of bioinformatics, in particular to a method and device for detecting microsatellite instability based on next-generation sequencing blood samples. Background technique [0002] Cancer is one of the most important non-communicable diseases in the world, and it is also a disease with a high mortality rate. In my country, nearly 4.3 million people are diagnosed with cancer every year, and more than 2.8 million people die of cancer. [0003] Anti-tumor targeted drugs and immune checkpoint inhibitors are currently more effective means of treating cancer. The currently recognized potential indicator for evaluating the efficacy of immune checkpoint inhibitor PD-1 is MSI (microsatellite instability). The calculation of MSI is based on Distribution of tandem repeats in tumors in somatic cells relative to blood leukocyte controls. It is generally recommended clinically that these drugs be tested for genes before bei...
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