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Methods, systems and probe sets for determining combinations of loci for detecting microsatellite instability

A technology of microsatellite instability and microsatellite loci, which is applied in biochemical equipment and methods, microbial measurement/inspection, etc., can solve problems such as lack of heterozygosity, inability to provide gene mutation information, and changes in peak size

Active Publication Date: 2022-05-17
元码基因科技(苏州)有限公司
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AI Technical Summary

Problems solved by technology

However, paired samples are required, and the number of gene combinations detected by it is small, the throughput is low, and specific gene mutation information cannot be provided.
In the judgment of the results, problems such as too strong or too little fluorescence, non-specific peaks, insignificant peak size changes, and loss of heterozygosity will be encountered.

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  • Methods, systems and probe sets for determining combinations of loci for detecting microsatellite instability
  • Methods, systems and probe sets for determining combinations of loci for detecting microsatellite instability
  • Methods, systems and probe sets for determining combinations of loci for detecting microsatellite instability

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Embodiment

[0084] In this example, a group of suitable MSI marker site combinations were screened, which greatly improved the accuracy and sensitivity of single-sample detection, and at the same time significantly reduced the detection cost of paired normal samples for joint detection in the single-sample process. details as follows.

[0085] Preliminary screening of 143 MS Markers (see Table 1), the screening principle is to select repeat units with microsatellite characteristics exceeding 10bp, highly polymorphic, and single-base repeat sequences with insertion / deletion mutations; including MSI-PCR capillary 6 markers used in electrophoresis (BAT25, BAT26, Mono27, NR24, NR26, NR27 based on Promega analysis system).

[0086] At the same time, in terms of probe design, there are two flanks on the left and right of the Marker repeat unit (repeat unit) (see figure 1 ) carried out the flanking two-stage flanking probe design, evaluated the marker capture efficiency and uniformity, and the ...

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Abstract

The invention discloses a method, a system and a probe set for determining a site combination for detecting microsatellite instability. The method is a method using a single tumor sample and based on next-generation sequencing technology, which includes the following steps: (1) preliminary screening to obtain a candidate locus set composed of multiple microsatellite loci; and (2) calculating the candidate locus set The contribution degree of each microsatellite site to the MSI status, and sort the microsatellite sites in the candidate site set according to the contribution degree, take the top n microsatellite sites to form the screening site set, and use the screening site set The sample MSI scores of the two groups of samples MSI-H and MSS were calculated, and the required locus combinations were obtained according to the sample scores. The site combination of the present invention can not only improve the accuracy and sensitivity of microsatellite state detection, but also greatly reduce the detection cost of a single-sample process.

Description

technical field [0001] The invention relates to the field of gene detection, in particular to a site combination method, system and probe set for determining microsatellite instability. Background technique [0002] Microsatellites are uniformly distributed, short tandem repeats or simple repeats in eukaryotic genomes, generally composed of tandem repeat units of 1-6 nucleotides. If the mismatch repair (MMR) gene is mutated, it will not be able to repair the spontaneous high-frequency length variation in microsatellites in time, thus causing microsatellite instability (MSI), that is, microsatellite instability (MSI) caused by the failure of the DNA mismatch repair system. Insertion or deletion of repetitive sequences in satellite regions. [0003] In 2017, the FDA approved pembrolizumab for the treatment of patients with dMMR / MSI-H unresectable or metastatic solid tumors, and MSI became the world's first molecular marker to guide tumor immunotherapy. MSI is present in a va...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6886C12Q1/6869
CPCC12Q1/6886C12Q1/6869C12Q2535/122C12Q2525/151
Inventor 杨洲张吉娜刘金洋张美俊孙雪王伟伟田埂
Owner 元码基因科技(苏州)有限公司